edgeR: How is FDR calculated for logFC? (False Discovery Rate)
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jol.espinoz ▴ 40
@jolespinoz-11290
Last seen 5 months ago

I'm having difficulty conceptualizing how significance of logFC is calculated with `exactTest()` and `Benjamini-Hochberg` adjusted FDR calculation with `topTags()`.  

Let's say you had `100 genes` with `5 control replicates` and `5 experimental replicates`,  how are p-values for the logFC calculated and then how are they adjusted using the `Benjamini-Hochberg` method?  For example consider `gene_1`, what if the control samples for `gene_1` were: `u = [5, 6, 5, 7, 5]` and the experimental replicate samples for `gene_1` were: `v = [9, 10, 11, 10, 8]`.  Does the algorithm just do a t-test or wilcoxon between `log2(u)` and `log2(v)` to get the p-values?  If so, wouldn't you need quite a bit of samples to get a reliable p-value? 

Is this how the p-value is calculated? If so, how the FDR calculated from this?  Sorry for all the questions, I'm just having trouble visualizing it.  I just ran `edgeR` on a dataset with 3 control replicates and 3 experimental replicates.  I'm not sure how the p-values and the FDR values are calculated and I'm trying to avoid blackboxing (i.e. using algos I don't understand conceptually).

edgeR bioconductor fdr statistics differential gene expression • 3.9k views
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@james-w-macdonald-5106
Last seen 4 hours ago
United States

There's no need to 'blackbox' anything. There is a user's guide that explains all, along with references if you really want to get down to the nitty gritty.

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Thanks for that!  So does it use a negative binomial distribution of the controls and then find the likelihood of the experimentalsnto fit that model? 

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