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<h1 class="title toc-ignore">Quantile-normalize intensity measurements</h1>
<h4 class="author"><em>Joyce Hsiao</em></h4>
</div>
<!-- The file analysis/chunks.R contains chunks that define default settings
shared across the workflowr files. -->
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<p><strong>Last updated:</strong> 2017-12-01</p>
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<p><strong>Code version:</strong> 55b4e74</p>
<hr />
<div id="introduction" class="section level2">
<h2>Introduction</h2>
<p>Previously when investigating measurement variation (GFP/RFP/FAPI), we learned that there’s significant variation between batches in the distributions of background-corrected pixel intensites. See <a href="../docs/images-qc-labels.html">here</a>.</p>
<p>In this document, I apply quantile normalization to intensity measurements. Bad news, it did not work well. While quantile normalization helps to remove variation between batches in intensity measurements, but by doing so, we increases the variation between individuals. The cells do not form any clusters in the Green versus Red plot. In hindsight, this seems to make sense. By normalizing samples within plate, we artifically inflated differences between individuals…</p>
<p>Next to try linear mixed model…</p>
<hr />
</div>
<div id="load-packages-and-data" class="section level2">
<h2>Load packages and data</h2>
<pre class="r"><code>library(data.table)
library(dplyr)
library(ggplot2)
library(cowplot)
library(wesanderson)
library(RColorBrewer)
library(Biobase)</code></pre>
<p>Name all plates.</p>
<pre class="r"><code>plates <- c("18511_18855","18855_19101","18855_19160","18870_18511",
"18870_18855","18870_19101","18870_19160","19098_18511",
"19098_18870","19098_19160","19101_18511","19101_19098",
"19160_18870","19101_19160","19160_18511", "18855_19098")</code></pre>
<p>Combine intensity stats from different plates.</p>
<pre class="r"><code># make the negative ones be the samllest one within its own plate
ints <- do.call(rbind, lapply(1:length(plates), function(index) {
tmp <- readRDS(paste0("/project2/gilad/fucci-seq/intensities_stats/",plates[index],".stats.rds"))
tmp <- data.frame(plate=plates[index],
well=as.character(droplevels(tmp$wellID)),
rfp.sum.zoom.mean.log10=log10(tmp$rfp.sum.zoom.mean),
gfp.sum.zoom.mean.log10=log10(tmp$gfp.sum.zoom.mean),
dapi.sum.zoom.mean.log10=log10(tmp$dapi.sum.zoom.mean))
tmp$rfp.sum.zoom.mean.log10[which(tmp$rfp.sum.zoom.mean.log10 == "NaN")] <- min(tmp$rfp.sum.zoom.mean.log10, na.rm=TRUE)
tmp$gfp.sum.zoom.mean.log10[which(tmp$gfp.sum.zoom.mean.log10 == "NaN")] <- min(tmp$gfp.sum.zoom.mean.log10, na.rm=TRUE)
tmp$dapi.sum.zoom.mean.log10[which(tmp$dapi.sum.zoom.mean.log10 == "NaN")] <- min(tmp$dapi.sum.zoom.mean.log10, na.rm=TRUE)
return(tmp)
}) )</code></pre>
<p>Load the expression set info.</p>
<pre class="r"><code>eset_fls <- list.files("../data/eset", full.names=TRUE)
anno <- do.call(rbind, lapply(1:length(eset_fls), function(index) {
eset_index <- readRDS(eset_fls[[index]])
pdata_index <- pData(eset_index)
return(pdata_index)
}))
# make unique id in both
ints$unique <- paste0(ints$plate,"_",as.numeric(ints$well))
anno$unique <- paste0(anno$image_individual,"_",anno$image_label)
subset_index1 <- which(anno$unique %in% ints$unique)
anno_subset <- anno[subset_index1,]
subset_index2 <- match(anno_subset$unique, ints$unique)
ints_tmp <- ints[subset_index2,]
all.equal(ints_tmp$unique, anno_subset$unique)</code></pre>
<pre><code>[1] TRUE</code></pre>
<pre class="r"><code>ints_tmp$chip_id <- anno_subset$chip_id</code></pre>
<hr />
</div>
<div id="densit-plots" class="section level2">
<h2>Densit plots</h2>
<p>First, look at the distribution of all batches combined versus each batch.</p>
<pre><code>Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
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<p><img src="figure/images-normalize-quantile.Rmd/unnamed-chunk-5-1.png" width="672" style="display: block; margin: auto;" /></p>
<hr />
</div>
<div id="normalization" class="section level2">
<h2>Normalization</h2>
<p>Code for one single sample</p>
<pre class="r"><code>my_quantnorm <- function(reference, sample, span=.01) {
# quantiles for intensities all samples across plates
quants_reference <- quantile(reference, probs=seq(0,1,span))
# intensities for a given plate
# quantiles for intensities at each plate
quants_sample <- quantile(sample, probs=seq(0,1,span))
# empty vector for normalized values
sample_normed <- vector("numeric", length=length(sample))
for (index in 1:length(sample)) {
# compare the sample intensity values with the refernece sample intensity values
# at each quantile; get the closes reference quantlie in terms of measurement values
sample_order <- names(which.min(abs(sample[index]-quants_sample)))
# get the reference intensity value of the closet quantile
ref_order_value <- reference[which(names(quants_reference)==sample_order)]
# assign the reference intensity value to the sample
sample_normed[index] <- ref_order_value
}
return(sample_normed)
}</code></pre>
<p><strong>Choose smoothing parameter for RFP</strong></p>
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Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.</code></pre>
<p><img src="figure/images-normalize-quantile.Rmd/unnamed-chunk-7-1.png" width="672" style="display: block; margin: auto;" /></p>
<p><strong>Choose smoothing parameter for GFP</strong></p>
<pre><code>Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.</code></pre>
<p><img src="figure/images-normalize-quantile.Rmd/unnamed-chunk-8-1.png" width="672" style="display: block; margin: auto;" /></p>
<p><strong>Choose smoothing parameter for DAPI</strong></p>
<pre><code>Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.</code></pre>
<p><img src="figure/images-normalize-quantile.Rmd/unnamed-chunk-9-1.png" width="672" style="display: block; margin: auto;" /></p>
<p><strong>Normalize intensity for each channel</strong></p>
<p>DAPI choose .001; Green choose .01; Red choose .01</p>
<pre><code>Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.</code></pre>
<p><img src="figure/images-normalize-quantile.Rmd/unnamed-chunk-10-1.png" width="672" style="display: block; margin: auto;" /></p>
<p>After normalization: Green versus Red by individual</p>
<pre><code>Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.</code></pre>
<p><img src="figure/images-normalize-quantile.Rmd/unnamed-chunk-11-1.png" width="1152" style="display: block; margin: auto;" /></p>
<p>Before normalization: Green versus Red by individual</p>
<pre><code>Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.
Warning in structure(NULL, class = "waiver"): Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
Consider 'structure(list(), *)' instead.</code></pre>
<p><img src="figure/images-normalize-quantile.Rmd/unnamed-chunk-12-1.png" width="1152" style="display: block; margin: auto;" /></p>
<hr />
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<pre><code>R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.2 (Nitrogen)
Matrix products: default
BLAS: /home/joycehsiao/miniconda3/envs/fucci-seq/lib/R/lib/libRblas.so
LAPACK: /home/joycehsiao/miniconda3/envs/fucci-seq/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] Biobase_2.38.0 BiocGenerics_0.24.0 RColorBrewer_1.1-2
[4] wesanderson_0.3.2 cowplot_0.9.1 ggplot2_2.2.0
[7] dplyr_0.7.4 data.table_1.10.4-3
loaded via a namespace (and not attached):
[1] Rcpp_0.12.13 knitr_1.16 bindr_0.1 magrittr_1.5
[5] munsell_0.4.3 colorspace_1.3-2 R6_2.2.2 rlang_0.1.4
[9] plyr_1.8.4 stringr_1.2.0 tools_3.4.1 grid_3.4.1
[13] gtable_0.2.0 git2r_0.19.0 htmltools_0.3.6 lazyeval_0.2.0
[17] yaml_2.1.14 rprojroot_1.2 digest_0.6.12 assertthat_0.1
[21] tibble_1.3.4 bindrcpp_0.2 glue_1.2.0 evaluate_0.10
[25] rmarkdown_1.6 labeling_0.3 stringi_1.1.2 compiler_3.4.1
[29] scales_0.4.1 backports_1.0.5 pkgconfig_2.0.1 </code></pre>
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