Question: What's the difference between DESeq and EdgeR?
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gravatar for guoxuantong
4 weeks ago by
guoxuantong10
guoxuantong10 wrote:

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?

rna-seq R software • 169 views
ADD COMMENTlink modified 4 weeks ago by i.sudbery11k • written 4 weeks ago by guoxuantong10
2
gravatar for i.sudbery
4 weeks ago by
i.sudbery11k
Sheffield, UK
i.sudbery11k wrote:

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.

ADD COMMENTlink written 4 weeks ago by i.sudbery11k

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?

ADD REPLYlink written 4 weeks ago by guoxuantong10
1

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

ADD REPLYlink written 4 weeks ago by ATpoint46k
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