What's the difference between DESeq and EdgeR?

Question

[Novogene]

I have one question about the RNA-seq analysis software and pipeline. What's the best analysis software for gene differential expression? What's the difference between DESeq and EdgeR?

Answer 1

[i.sudbery]

There are some small technical differences in DESeq and edgeR, like how they do normalization, the precise details of how they estimate dispersion, and how they encode contrasts. DESeq2 also does a bunch of things automatically that you'd have to specifically ask for in edgeR, like independent filtering and outlier detection (this might be good or bad depending).

But in general DESeq2 and edgeR are more or less the same - it doesn't really matter which you use.

[Novogene]

Thank you for answering. So I have three groups of sample, and one is the control and the other two are fed with two diff small molecule drugs. Three replicates in each group. which one do you recommend to use for expression analysis for me? and why?

[ATpoint]

I suggest you go through the manuals of both and then simply see which one you feel more comfortable with, simple as that.