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16 months ago by
nia10 wrote:

Dear fellows,

I need your suggestion i have around 200 degs which i retrieved after doing its linear modeling , i submit the genes in (genecodis3) tool for the biological and molecular enrichment analysis and i got around 250 GO annotations is it fine i just take top 10 for table (fdr<0.05) (test=hyper geometrical test)

ADD COMMENTlink modified 16 months ago by Robert Castelo2.2k • written 16 months ago by nia10
gravatar for Robert Castelo
16 months ago by
Robert Castelo2.2k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.2k wrote:


It's unclear to me to what Bioconductor package are your referring to when you talk about the "genecodis3 tools" as a text-free search among the software packages does not give any hit.

About the general question on how to select enriched GO terms, there are many options, just think for instance that you're talking about the top-10 GO terms without defining what is the metric you use to rank them.

If you're going to select GO terms on the basis of multiple test correction on a one-tailed Fisher's exact test p-value, which is a tricky business given the overlapping nature of GO terms and the consequently lack of independence of the raw p-values assumed by correction methods such as FDR, I would avoid testing GO terms annotated to fewer than 5 and more than 300 genes in your data set. This should alleviate the burden of the multiple test correction, while likely discarding GO terms for which either the representation in your data is too small (< 5 genes) to do a reliable inference, or too large (> 300) to draw useful conclusions. You may of course use different thresholds than the ones I'm proposing.

Regarding the way in which you may rank GO terms, once you've selected them, i'd use the odds-ratio of enrichment.



ADD COMMENTlink written 16 months ago by Robert Castelo2.2k
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