Question

Using Gage and pathview with previously processed data

0

Entering edit mode

bsguida • 0

@bsguida-9785

Last seen 8.8 years ago

Hello all,

Thanks for reading. I have a RNA-SEQ data set which I have already processed, I now have a list of up and down-regulated genes with p-values, fold changes, and KO numbers (already ran proteins through KEGG) which contains about 850 genes. I want to run this data through Gage/Pathview to look at any metabolic pathway changes which have occurred under my specific treatment. The gage and pathview vignettes are not commented enough for me (an R newbie) to figure out where I can enter the pipeline with my data file. Without adequate programming comments in the manuals I'm currently unable to follow the procedures.

I'd greatly appreciated any help anyone can give.

Thanks!

Brandon

pathview gage r kegg rnaseq • 1.4k views

ADD COMMENT • link updated 8.7 years ago by Luo Weijun ★ 1.6k • written 8.8 years ago by bsguida • 0

score 0 · Answer 1 · 2016-02-24

You will need the full data set or differential expression scores (fold changes, test statistics or p-values) with all genes included to run GAGE. If you only have access to the list of pre-selected genes, you can do some overrepresentation test to select significant pathways, and then visualize the pre-selected genes in these pathways using Pathview. Anyway, you need to be familiar with R to use these packages.