I finished my RNAseq analyses, and i have problems to model it. For example i have two comparisons A/Control and B/Control, i have the fold change for the gene expression, and the pval. Between these two comparisons i have genes unregulated in both condition and i would represent it with Ven-Diagram and calculate a pval of this overlapping using hypergeometric distribution.
I read this post on Biostars: Probability Of Gene List Overlap, but instead of him, i don't have the same number of genes between the both comparison (due to filtering data). Does somebody know how if i must use it with the smallest number of genes between both comparison, or if i need to weight the total number of genes?
Thanks a lot, and sorry for my english ;)