Hi there, This is my first time doing GO enrichment and I am a little confused and could do with some help.
I'm doing a meta analysis of diff. tissues and now trying to do a GO analysis of the Fisher's findings.
I've found GoExpress and topGO as tools, but their instruction guides are a mystery to me. I am not sure what they want and they also ask for annotations, which is a little tricky in a meta analysis of different platforms?
For example, running the below gives me the error code "invalid genes selected".
DE_genes_CD <- subset(blood_sorted, Fishers.P.Value < 0.001)$Symbol back_genes_idx <- genefinder(as.matrix(blood), as.character(DE_genes_CD), method="manhattan", scale="none")
I'm sure I'm overlooking something or not approaching/understanding this the right way.
Any help/hints/code would be much appreciated!!!!