Question: DE comparison between different softwares
gravatar for Constantine
5.1 years ago by
Constantine280 wrote:


I'm looking for DE between a mutant  and a WT cell line - 3 replicates for each condition.

I've been using 2 different R packages: edgeR and limma

If I set an FDR <0.01 and abs(logFC) > 0.3 I get for:

edgeR:  ~100 DE genes

limma:  ~300 DE genes

How do I assess whether the extra 200 DE genes I get in limma are actually genuine and not false positives?

When I was analsying expression microarrays I used to test whether a normalisation method was efficient by plotting QQ plots of the P.values. However, doing linear regressions on this dataset doesn't seem to be working as I expected :/

Any advice would be much appreciated



sequencing rna-seq next-gen • 1.3k views
ADD COMMENTlink modified 5.1 years ago by Devon Ryan97k • written 5.1 years ago by Constantine280
gravatar for Devon Ryan
5.1 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

You're presumably going to be doing some qPCR in additional samples anyway, so choose a few of the limma-only genes and see what happens. Also, have a look at whether the limma-only genes are just slightly sub-threshold in edgeR. Shifts around the border of significance are pretty common causes of things like this.

ADD COMMENTlink modified 5.1 years ago • written 5.1 years ago by Devon Ryan97k

To add to the second point, a good article on this topic is "The Difference Between "Significant" and "Not Significant" is not Itself Statistically Significant". I think it's very important to keep this fact in mind when analyzing these types of results.

ADD REPLYlink modified 12 months ago by _r_am31k • written 5.1 years ago by matted7.3k
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