Hi Matt and Nadia,

For almost a year, I was using goseq as a generalized enrichment tool (leveraging the gene length bias correction implemented there, thank you) using my custom gene sets this way:

goseq(myData, genome=NULL, id=NULL, gene2cat = MyVeryOwnGeneCategorization, method="Sampling", repcnt = 100000)

After recent update to version 1.18.0, the pipeline crashed and returned this:

################################
Error in .testForValidKeys(x, keys, keytype) :
 None of the keys entered are valid keys for 'GOID'. Please use the keys method to see a listing of valid arguments.
################################

It looks like the current version became explicitly restricted to use of the pre-defined geneset categories (I see "test.cats" argument that defaults to c("GO:CC", "GO:BP", "GO:MF") in the manual and when I looked at the code itself, it seems to accept "KEGG" as well and return an error in any other case).

This restriction dramatically narrows the applicability of goseq. Could this be changed in the upcoming version?

Thank you,

Oleg

This response is a bit late, but for those interested, I was not able to recreate this issue.

If you can send me the results of sessionInfo() and a small example with data and commands run, I'll look into it more detail.

Cheers,

Nadia.