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
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.