Question: Using Gage and pathview with previously processed data
gravatar for bsguida
2.6 years ago by
bsguida0 wrote:

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.




ADD COMMENTlink modified 2.6 years ago by Luo Weijun1.4k • written 2.6 years ago by bsguida0
gravatar for Luo Weijun
2.6 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
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.
ADD COMMENTlink written 2.6 years ago by Luo Weijun1.4k
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