Go Enrichment Rnaseq: Nothing! (Goseq)

Question

[Pfs]

Hello!

I used goseq package to do GO-enrichment of RNASEQ data. The up- and down-regulated genes are not enriched in any category if I use the BH (FDR) correction. Is that a possible situation or is it more likely I made some mistake? If the latter, what should I look for?

Thanks in advance.

[seidel]

Have you tried a positive control? Try spiking one of your gene lists with a bunch of ids from a particular category, then run goseq and see if it hands that category back to you. Otherwise it could simply the result of your experiment. If the null hypothesis were true (i.e. your up and down regulated genes are really no different than a randomly chosen set), would you expect an enrichment?

[David Quigley]

@seidel : I would re-post that comment as an answer, since it's a good answer and you should get credit for the up-vote.

[Russh]

It's quite feasible. Can you use goSlim terms in goseq?

Answer 1

[seidel]

Have you tried a positive control? Try spiking one of your gene lists with a bunch of ids from a particular category, then run goseq and see if it hands that category back to you. Otherwise it could simply be the result of your experiment. If the null hypothesis were true (i.e. your up and down regulated genes are really no different than a randomly chosen set), would you expect an enrichment?