Hi all, I'm right now working with a RNA-seq raw count data file (in .txt format). It's a matrix of ~50,000 genes (row) and 8 samples (column).

My assignment is to get differential gene ontology and gene set enrichment. But I'm not really sure what it means by that. I'm trying to use R for this task, and when I googled for gene ontology analysis in R, there are several packages that are designed to get GO and GSE. But, if I'm starting with a raw count data file, which package do you recommend for this task?

Also, if one wants to see gene ontology, what exactly they mean by that (probably like an example of ideal results)?

I'm really new to bioinformatics and R, so please explain from the scratch.

Thanks a lot!!

Here is a complete analysis workflow for an RNA-seq dataset:

https://f1000research.com/articles/5-1438

This example analysis includes both gene ontology and gene set enrichment analyses as well as two different types of MA plots.

maybe you can follow this workflow: https://github.com/twbattaglia/RNAseq-workflow