Question: Go Enrichment Rnaseq: Nothing! (Goseq)
4
gravatar for Pfs
8.8 years ago by
Pfs510
United States
Pfs510 wrote:

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.

enrichment rna • 2.5k views
ADD COMMENTlink modified 4.8 years ago by Biostar ♦♦ 20 • written 8.8 years ago by Pfs510

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?

ADD REPLYlink written 8.8 years ago by seidel7.0k

@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.

ADD REPLYlink written 8.8 years ago by David Quigley11k

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

ADD REPLYlink written 8.8 years ago by Russh1.2k
8
gravatar for seidel
8.8 years ago by
seidel7.0k
United States
seidel7.0k wrote:

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?

ADD COMMENTlink written 8.8 years ago by seidel7.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1138 users visited in the last hour