Question: number of grouping affect log2 fold change in DESeq2 analysis?
1
gravatar for star
4.3 years ago by
star270
Netherlands
star270 wrote:

I have RNA-seq data for samples in 10 different groups and I would like to find deferentially expressed genes. I have used Deseq2 R package. The deferentially expressed genes have FDR between 0.03 and 0.05. I checked log2FC and found it is low value in most deferentially expressed genes. How I can explain this? Why genes with low log2FC are found to be deferentially expressed? Also I have checked the normalized count and I couldn't find any reason!

edger log2fc deseq2 R • 1.4k views
ADD COMMENTlink modified 4.3 years ago by Devon Ryan98k • written 4.3 years ago by star270

How come no differentially expressed gene has fdr below 0.03? I guess you have some kind of filtering going on ..

ADD REPLYlink written 4.3 years ago by vivekbhr630
3
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

The number of groups you're using suggests that there's a lot of variance shrinkage going on, which is why you're picking up low fold-change differences. My guess is that you have relatively few replicates per group, which is causing aggressive fold-change shrinkage.

ADD COMMENTlink written 4.3 years ago by Devon Ryan98k
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