1 Basic DESeq2 results exploration

Project: SRP009615.

2 Introduction

This report is meant to help explore DESeq2 (Love, Huber, and Anders, 2014) results and was generated using the regionReport (Collado-Torres, Jaffe, and Leek, 2016) package. While the report is rich, it is meant to just start the exploration of the results and exemplify some of the code used to do so. If you need a more in-depth analysis for your specific data set you might want to use the customCode argument. This report is based on the vignette of the DESeq2 (Love, Huber, and Anders, 2014) package which you can find here.

2.1 Code setup

This section contains the code for setting up the rest of the report.

## knitrBoostrap and device chunk options
load_install('knitr')
opts_chunk$set(bootstrap.show.code = FALSE, dev = device)
if(!outputIsHTML) opts_chunk$set(bootstrap.show.code = FALSE, dev = device, echo = FALSE)
#### Libraries needed

## Bioconductor
load_install('DESeq2')
if(isEdgeR) load_install('edgeR')

## CRAN
load_install('ggplot2')
if(!is.null(theme)) theme_set(theme)
load_install('knitr')
if(is.null(colors)) {
    load_install('RColorBrewer')
}
load_install('pheatmap')
load_install('DT')
load_install('devtools')

## Working behind the scenes
# load_install('knitcitations')
# load_install('rmarkdown')
## Optionally
# load_install('knitrBootstrap')

#### Code setup

## For ggplot
res.df <- as.data.frame(res)

## Sort results by adjusted p-values
ord <- order(res.df$padj, decreasing = FALSE)
res.df <- res.df[ord, ]
res.df <- cbind(data.frame(Feature = rownames(res.df)), res.df)
rownames(res.df) <- NULL

3 PCA

## Transform count data
rld <- tryCatch(rlog(dds), error = function(e) { rlog(dds, fitType = 'mean') })

## Perform PCA analysis and make plot
plotPCA(rld, intgroup = intgroup)