I want to look at an RNA-seq data-set on 1 condition to look for expressed genes. As there is only one condition, I can’t perform differential analysis.

The only thing I can think to do is set a threshold (i.e. all replicates must have > 10 gene counts) then say these are expressed. But I don’t think this is a very good way of doing it.

Do you know of any better ways that we can do this?

Thank you for any idea


If you've got enough replicates (ideally at least 6, but can be done with 3), you should be able to do a Variance-stabilised Transformation using DESeq2:

vsd <- vst(dds, blind=FALSE)
rld <- rlog(dds, blind=FALSE)
head(assay(vsd), 3)

More details on this can be found in the DESeq2 Vignette:



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