DESeq output from RNA-seq

Question

[a.james]

Hello All

I have a set of DE gens from DESeq (filtered with p_value<=0.05, FDr<=0.1 and Logfoldchange for up and down regulated genes )In my case I filtered and taken this as my DE genes.

Now I am a little bit confused here. Is this genes differently expressed over my treatment samples(leu) or control(Normal). My design looks like this from one example

single_patDesign = data.frame(row.names = colnames( single_pat ),condition = c("Leu","Leu","Normal"))

where I have 2 leukemic samples and one normal sample.I wanted to find out which all genes are expressed specifically in Leukemic samples and control.

Thank you

Answer 1

[Devon Ryan]

A few things. Firstly, DESeq (and pretty much every similar tool) won't give you genes specific to a given condition, but genes differentially expressed by condition (there's a rather large difference in meaning there). Secondly, your question can be rephrased as, "if a log2 fold change is positive, what's that relative to?" The simplest way to check is to simply look at the normalized counts for one of the differentially expressed genes and the answer will be immediately apparent (or just look at things in IGV).

BTW, you should really be using DESeq2. It'll also label things so you know what's being used as the numerator for the fold-change.

[a.james]

Thank you so much for the reply. Ok, I will try with DEseq2.