I would like to create a "representative" random set of lets say 30-100 mouse genes as a reference set for some enrichment analysis. Do you have any ideas how to do this?
Hana, one idea is to make 100 different random reference sets of 30-100 genes each (the size chosen to match the size of your test set).
That way, you will be able to calculate the 'average' expected values relating to a random set of genes, but you will also be able to calculate the distribution of those values - this will give you a more powerful way to statistically test whether your test set is truly enriched compared to random sets.
Jonathan: Thanks a lot, this is what I was thinking about. I guess there could be some R packages to do that?
Rohan: A bit ashamed... I guess I should think more before posting here. Although - since this is a new field for me, I was not aware about all the things my question could refer to.
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