RNA-seq DE analysis noob here so please bear with my silly question!
So, I have tximported my salmon data of paired-end RNA seq reads and I am trying to use DESeq2 to analyze the differential expression for two conditions (screen and treatment) in 8 different patients.
I use this bit of code:
coldata<-data.frame(con=s2c$condition) rownames(coldata)<-colnames(txi) dds <- DESeqDataSetFromTximport(txi, colData=coldata, design= ~con) dds <- dds[ rowSums(counts(dds)) > 1, ] dds<-DESeq(dds) res<-results(dds)
but I get padj values in all my genes around 0.9!
On the other hand, if I use replicates (patient1, patient2 and so on) I got some significant padjs but my MA plot is a small vertical line!
Maybe I shouls use both factors (replicate and condition) on my design? How can I do that?
Could someone please help me understand what I am doing wrong?
Thank you very much!