Question: number of grouping affect log2 fold change in DESeq2 analysis?
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3.7 years ago by
star230 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 • 1.3k views
ADD COMMENTlink modified 3.7 years ago by Devon Ryan95k • written 3.7 years ago by star230

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

ADD REPLYlink written 3.7 years ago by vivekbhr550
gravatar for Devon Ryan
3.7 years ago by
Devon Ryan95k
Freiburg, Germany
Devon Ryan95k 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 3.7 years ago by Devon Ryan95k
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