I am using following code for my expression analysis from the edgeR package.
data = read.table("mirna.readcout", header=T, row.names=1, com='')
col_ordering = c(1,2,3,4,5,6)
rnaseqMatrix = data[,col_ordering]
rnaseqMatrix = round(rnaseqMatrix)
rnaseqMatrix = rnaseqMatrix[rowSums(rnaseqMatrix)>=2,]
conditions = factor(c(rep("Set1", 3), rep("Set2", 3)))
exp_study = DGEList(counts=rnaseqMatrix, group=conditions)
exp_study = calcNormFactors(exp_study)
exp_study = estimateCommonDisp(exp_study)
exp_study = estimateTagwiseDisp(exp_study)
et = exactTest(exp_study)
tTags = topTags(et,n=NULL)
write.table(tTags, file='mirna.Set1_vs_Set2.edgeR.DE_results', sep=' ', quote=F, row.names=T)
I would like to get the normalised value Per Group (ie. Set1 & Set2) which is used in the exactTest. How can I get that? In otherwords the data which is used to calculate logFC?.
Looking forward for your reply, Thank you very much for your time.