So, I am working on a method. From this method I can get a small subset of differentially expressed genes. I only get around ~100 genes compared to if I don't use any subsetting metjhod, around ~3000. From this result, I compare the enrichment analysis using Enrichr, DAVID, and other similar web based enrichment analysis tools.
My question is, how can I say my subsetting method can extract more important information compare to without subsetting at all? I noticed that the enrichment result from subset give something important related to cancer in the first five or ten row while ordinary method without subsetting produce a lot of result which I'm not really sure whether it is relevant or not with cancer development.
Any suggestion how to test and to prove that my method of subsestting is better? Thank you.