Hi, I'm currently doing GSEA with my list of differentially expressed genes obtained with DeSeq2. I'm new in this kind of analysis and I'm currently encountering strange results.
To give you some background, I compared two basic conditions : treated vs untreated. I would like to know which genes are differentially expressed in the treatment condition. This treatment in the first condition induce apoptosis and it's known for that. I'm trying to find the genes which has been up / down regulated and the pathway impacted which are responsible of apoptosis.
The fact is, when I'm doing GSEA following the tutorial of ClusterProfiler, the pathways associated with apoptosis are down regulated. It seems to be inverse to what happens biologically.
Do you have any ideas to check if I didn't done something wrong ? Maybe I didn't compare my conditions in the right way with DeSeq2 and the over expressed genes are down expressed genes in fact ?
In DeSeq2 I made this contrast :
res <- results(dds, contrast = "group", "treated","untreated")
By doing this does DeSeq2 gives me over expressed genes in treated condition or untreated condition ? The Log2(FC) are calculated as treatment over control or the other way around ?