When I use different tools, I get different lists of genes! g:Profiler vs gageData and more. The thing is I have not yet been able to find an up to date list of genes for this gene set.
I want to do it in R preferably, and just get a vector of all the genes from geneontology.org officially, not through any of the 3rd party sites. I tried downloading some of their tables but the results gave bad gene sets. I did not manage to find an up to date .gmt file, the mSigDB gmt files for GO terms are from 2016
EDIT: I have been able to find the list of genes here http://amigo.geneontology.org/amigo/term/GO:0000002 by setting the correct parameters, 22 genes in human. However, I am still unable to find a download of up to date annotation files/gmt files that give the same results.
What is the link between your title and question?
Hi uaakash.mumbai, welcome to Biostars. I deleted your spamming action in this thread Polymorphic sites detection from MiSeq data of 3 individuals. I hope this was just an unfortunate start in our community. Please keep it clean and stay professional. You are welcome to ask all kinds of questions and to help others. Cheers!