FDR correction

[julien-roux]

(Not really an issue, but more a discussion post):

It is not clear if correcting the p-values to get a FDR is valid: the different tests we perform are not independent because of propagation of data through the ontology. The decorrelation methods of topGO make them even less independent (see section in topGO manual). For now I don't see any solution to this problem, and my feeling is that the FDR is conservative in this setting, so this is not a critical problem (but it is just a feeling I might be wrong).

Another problem is that depending on the tissues, the power of the test changes greatly. The more genes mapped to a term, the more power has our test. This can also affect our FDR correction. An idea is to incorporate this is FDR calculations, as done in the IHW package: http://bioconductor.org/packages/devel/bioc/vignettes/IHW/inst/doc/introduction_to_ihw.html. This is something we could easily add to BgeeDB! The covariate vector being the number of genes mapped to each term.