hello. I am working with a non-model organism (although it has had its genome sequenced) and am interested in looking at functional enrichment of differentially expressed genes. I did blastx against an insect database and then put the results into an XML file to retrieve the protein, which I then loaded into blast2go to map, annotate and then run the fisher's exact test (I used standard settings for these, with an e value cut off of 1x10-6)
However, I have a very low number of reads mapped and annotated in total. So when it comes to looking at my Fisher's exact test, I have a very low reference set and probably low statistical power. Is it normal to have this low number of genes mapped and annotated for a non-model organism, or should it generally be higher than this?
Thanks!
Hi, did you solve this problem? I am facing a similar issue. The database I used was uniprot.