Question: edgeR: How is FDR calculated for logFC? (False Discovery Rate)
gravatar for jol.espinoz
2.8 years ago by
jol.espinoz20 wrote:

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).

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by jol.espinoz20
Answer: edgeR: How is FDR calculated for logFC? (False Discovery Rate)
gravatar for James W. MacDonald
2.8 years ago by
United States
James W. MacDonald51k wrote:

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.

ADD COMMENTlink written 2.8 years ago by James W. MacDonald51k

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? 

ADD REPLYlink written 2.8 years ago by jol.espinoz20
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