I am using microarray analysis (e.g. Affymetrix) to identify differentially express genes (DEGs). I set two conditions to define the DEGs: (1) fold changes of >1.5 or <0.5; (2) q-value < 0.05 (I am using q-value to account for multiple comparisons).
Once I have the list of DEGs defined, and I am doing functional annotation and enrichment analysis (e.g. gene ontology and pathway enrichment analysis) with DAVID. My question is: to define what functional groups are significantly enriched, should I use p-values or q-values in the second round of analysis?
My intuition says that, since I already selected the DEGs by using q-value, the resulting list of genes has already been corrected for multiple testing. Thus, I should just focus on p-values for gene ontology and pathway enrichment analysis.
I have gone through the literature, and I have read papers using both strategies: DEGS with q-values and functional annotation with p-values, and others using q-values always.