Do edger, limma and deseq2 can be used with datasets from UMIs

Question

[ve9]

Hi,

my question is regarding the most common diff. expr. tools used (edger, deseq2, limma). As they are created before UMIs existed (where the overall set of data includes quite low copy numbers on all entries which seem like rare low expressed genes) did such data can be used with their statistical methods and normalization and get proper DEG results? I'm not a statistician but know that changing the scale of the data, dispersion, etc may cause bias in the results?

Answer 1

[Devon Ryan]

UMI counts will work perfectly fine for these tools and should actually better match the statistical assumptions underlying them than regular read counts (due to the additional noise from PCR duplicates here). The issue is more when you get to drop-outs (missed signal), which can occur in things like scRNA-seq. In practice that still seems to be handled well enough by these tools.

[ve9]

Thanks for the info!