I have been tasked with looking for differential expression in a colleague's data set. The data set consists of 24 RNAseq samples, made up of 4 groups of 6 samples.
I used DESeq2 with everything set default, and I am a little concerned with my results.
We have very few genes differentially expressed (2-4 per comparison), and those that seem to be from comparisons that are 0s compared to maybe 2 samples with counts when comparing between a treatment (named BOTH) group of 6 and group of 6 control (named CLEAN).
Is it valid to use these genes where maybe 2 samples are driving DE between the groups?