I have collections of probe/genes from 3 different conditions (e.g. stimulated by chemical1 2 3). They are already selected based on some fold change threshold. What I want to do now is to look at GO that are preferentially occur in each of the above conditions.
I face two following ways to do it, which I'm not sure which one is the correct one to do:
Obtain GO for each of the conditions together with the p-value of the GO term. Then perform clustering (hierarchical/knn) on these p-values.
Perform the clustering for the foldchange or the expression values. Then for each of the clusters determine the GO.
Your advices would be truly appreciated.
g.v.
1 answer
I would suggest option 3, performing the DE tests such that you answer the actual biological question you're trying to ask (e.g., chemical 1 vs. 2 or 1 vs. 2 and 3 as a group) and then calculate GO enrichment on that. You can then simply avoid clustering altogether and have more confident results.
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