**9.2k**wrote:

Hi,

I've a small question concerning differential expression analysis. So I've a 12 samples divided into three groups (A, B and C ). If a do that :

samples <- read.table("samples.txt",sep="\t",as.is=T) colnames(samples)<-c("sampleName","fileName","condition") dds1 <- DESeqDataSetFromHTSeqCount(sampleTable=samples,directory="./",design= ~ condition) dds1 <- DESeq(dds1) res <- results(dds1)

What will the p-value represent ? if it's significatif, is it because the gene of interest is up or down regulated in one of the three groups ?

To do pairwise comparison, I do that. Is it correct ?

res.A.B <- results(dds1, contrast=c("condition","A","B")) res.A.C <- results(dds1, contrast=c("condition","A","C")) res.B.C <- results(dds1, contrast=c("condition","B","C"))

Thanks

**97k**• written 6.1 years ago by Nicolas Rosewick ♦

**9.2k**