DESeq vs edgeR comparison

deseq-vs-edger.R

# Note: using the devel versions of both packages!
library(DESeq) # version 1.9.11
library(edgeR) # version 2.99.8
library(VennDiagram)

# Read in data ------------------------------------------------------------

## Use pasilla data
datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" )
datafile

## Read in the data making the row names the first column
counttable <- read.table(datafile, header=T, row.names=1)
head(counttable)

## Make metadata data.frame
meta <- data.frame(
  row.names=colnames(counttable),
  condition=c("untreated", "untreated", "untreated", "untreated", "treated", "treated", "treated"),
  libType=c("single", "single", "paired", "paired", "single", "paired", "paired"))
meta$condition <- relevel(meta$condition, ref="untreated")
meta

## Independent filtering?
# keep_cpm <- rowSums(cpm(counttable)>2) >=2
# keep_quantile <- rowSums(counttable)>quantile(rowSums(counttable), probs=.5)
# addmargins(table(keep_cpm, keep_quantile))
# counttable <- counttable[keep_cpm, ]

# DESeq -------------------------------------------------------------------

## Make a new countDataSet
d <- newCountDataSet(counttable, meta)

## Estimate library size and dispersion
d <- estimateSizeFactors(d)
d <- estimateDispersions(d)
plotDispEsts(d, main="DESeq: Per-gene dispersion estimates")

## Principal components biplot on variance stabilized data, color-coded by condition-librarytype
print(plotPCA(varianceStabilizingTransformation(d), intgroup=c("condition", "libType")))

## Fit full and reduced models, get p-values
dfit1 <- fitNbinomGLMs(d, count~libType+condition)
dfit0 <- fitNbinomGLMs(d, count~libType)
dpval <- nbinomGLMTest(dfit1, dfit0)
dpadj <- p.adjust(dpval, method="BH")

## Make results table with pvalues and adjusted p-values
dtable <- transform(dfit1, pval=dpval, padj=dpadj)
dtable <- dtable[order(dtable$padj), ]
head(dtable)

# edgeR -------------------------------------------------------------------

## Make design matrix
condition <- relevel(factor(meta$condition), ref="untreated")
libType <- factor(meta$libType)
edesign <- model.matrix(~libType+condition)

## Make new DGEList, normalize by library size, and estimate dispersion allowing possible trend with average count size
e <- DGEList(counts=counttable)
e <- calcNormFactors(e)
e <- estimateGLMCommonDisp(e, edesign)
e <- estimateGLMTrendedDisp(e, edesign) 
e <- estimateGLMTagwiseDisp(e, edesign)

## MDS Plot
plotMDS(e, main="edgeR MDS Plot")

## Biological coefficient of variation plot
plotBCV(e, cex=0.4, main="edgeR: Biological coefficient of variation (BCV) vs abundance")

## Fit the model, testing the coefficient for the treated vs untreated comparison
efit <- glmFit(e, edesign)
efit <- glmLRT(efit, coef="conditiontreated")

## Make a table of results
etable <- topTags(efit, n=nrow(e))$table
etable <- etable[order(etable$FDR), ]
head(etable)

## ~MA Plot
with(etable, plot(logCPM, logFC, pch=20, main="edgeR: Fold change vs abundance"))
with(subset(etable, FDR<0.05), points(logCPM, logFC, pch=20, col="red"))
abline(h=c(-1,1), col="blue")

# Comparison --------------------------------------------------------------

head(etable)
head(dtable)

addmargins(table(sig.edgeR=etable$FDR<0.05, sig.DESeq=dtable$padj<0.05))

merged <- merge(etable, dtable, by='row.names')
with(                     merged, plot(logFC, conditiontreated, xlab="logFC edgeR", ylab="logFC DESeq", pch=20, col="black", main="Fold change for DESeq vs edgeR"))
with(subset(merged, FDR<0.05),  points(logFC, conditiontreated, xlab="logFC edgeR", ylab="logFC DESeq", pch=20, col="red"))
with(subset(merged, padj<0.05), points(logFC, conditiontreated, xlab="logFC edgeR", ylab="logFC DESeq", pch=20, col="green"))
legend("topleft", xjust=1, yjust=1, legend=c("FDR<0.05 edgeR only", "FDR<0.05 DESeq & edgeR", "FDR>0.05"), pch=20, col=c("red", "green", "black"), bty="n")


# > sessionInfo()
# R version 2.15.0 (2012-03-30)
# Platform: i386-apple-darwin9.8.0/i386 (32-bit)
# 
# locale:
#   [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
# 
# attached base packages:
#   [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
#   [1] DESeq_1.9.11        lattice_0.20-10     locfit_1.5-8       
#   [4] Biobase_2.16.0      BiocGenerics_0.2.0  edgeR_2.99.8       
#   [7] limma_3.12.1        BiocInstaller_1.4.7
# 
# loaded via a namespace (and not attached):
#   [1] annotate_1.34.1      AnnotationDbi_1.18.1 DBI_0.2-5           
#   [4] genefilter_1.38.0    geneplotter_1.34.0   grid_2.15.0         
#   [7] IRanges_1.14.4       RColorBrewer_1.0-5   RSQLite_0.11.1      
#  [10] splines_2.15.0       stats4_2.15.0        survival_2.36-14    
#  [13] tools_2.15.0         XML_3.9-4            xtable_1.7-0