Hello, 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 sizes. Is there an R package that can use the existing annotation environments for running ANOVA? Kind regards, January -- -------- Dr. January Weiner 3 --------------------------------------

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: http://nar.oxfordjournals.org/content/early/2012/05/24/nar.gks461 Have you consider the roast method in the limma package: http://bioinformatics.oxfordjournals.org/content/26/17/2176 which has the flavor of an anova approach but fully acounts for inter- gene correlation. Best wishes Gordon ------------ original message ------------ [BioC] ANOVA for gene ontology analysis January Weiner january.weiner at gmail.com Wed Oct 17 13:36:36 CEST 2012 Hello, 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 sizes. Is there an R package that can use the existing annotation environments for running ANOVA? Kind regards, January ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}