DESeq2: impact of number of expressed genes in differential expression analysis
I have 10 RNA-seq samples in 2 groups (GroupA and GroupB), and 3 of GroupB have only a half of expressed genes (i.e. genes with count >0).
And I found that expression levels of all the lowly expressed genes in those samples were exaggerated (>10 times higher than other samples) after normalization in DESeq2.
I think discarding those samples are the best solution, but if I really have to keep them in the analysis what would be the best way to handle this situation?
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