[BioC] ANOVA for gene ontology analysis

Gordon K Smyth smyth at wehi.EDU.AU
Wed Oct 17 23:59:03 CEST 2012

Dear January,

I don't know entirely what you have in mind from your brief description, 
but it does sound like the method you are proposing would entirely ignore 
inter-gene correlations, which can be catastrophic, see:


Have you consider the roast method in the limma package:


which has the flavor of an anova approach but fully acounts for inter-gene 

Best wishes

------------ original message ------------
[BioC] ANOVA for gene ontology analysis
January Weiner january.weiner at gmail.com
Wed Oct 17 13:36:36 CEST 2012


I would like to test the significance of GO terms using ANOVA. Correct
me if I'm wrong, but I think that it makes sense to make a three
factorial ANOVA (where genes are one factor,  the experimental group
is the other, and the specific sample is the third) on a group of
selected genes (for example, group of genes belonging to a given GO
annotation group).

Clearly, this approach might have less power in case of small sample
sizes, but could be better than enrichment tests for larger sample

Is there an R package that can use the existing annotation
environments for running ANOVA?

Kind regards,

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