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Very less highly expressed genes in DGE analysis

I'm a beginner in DGE analysis, right now my dataset (which is bulk rna seq btw) has 12 samples (6 treated and 6 control). I'm using a combination of edgeR , voom and limma. while applying the filter; myCPM <- cpm(countdata)

head(myCPM)
thresh <- myCPM > 0.5
head(thresh)
table(rowSums(thresh))
keep <- rowSums(thresh) >= 2
summary(keep)

I'm getting only 1500 genes. I don't know if i should proceed with these. Can somebody pls help me with this???

dge analysis
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updated by fernando • fernando • written by ziraa • ziraa

Why is it that especially beginners always come with these off custom filters rather than just sticking to the edgeR (or limma) manual. Just take your matrix of raw counts, and run filterByExpr() on it, as suggested in the user guides. Assume that x was your matrix of raw counts, what is the output of summary(apply(x, 2, sum))?

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written by ATpoint ATpoint

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