GOseq and KEGG pathways analysis for mouse RNA-seq

Question

[trakhtenberg]

Hello,

We did GOseq on mouse RNA-seq but are having trouble with getting the KEGG pathways analysis to work in this pipeline. It is important for us to use it in the same pipeline because GOseq accounts for the gene length bias, and it suppose to be accounted for in the KEGG pathways analysis too when used in the same pipeline (that's why I cant use DAVID as it doesn't account for the gene length bias in KEGG pathways analysis). If this has worked for you or you know of a publication using this approach, please comment.

Thank you.

[Dr Reema Singh]

Could you explain this a little bit more like - what is the actual problem- using KEGG in Goseq OR importing KEGG data in GOseq? Because as far as I known Goseq manual has the complete description. The only problem I find is about the updated KEGG information, as KEGG is available on subscription for academic users.