retrieve kegg pathway abundances from gage analysis
2
0
Entering edit mode
Last seen 7.4 years ago
European Union

Hi!

I used gage in order to perform a pathway enrichment analysis, using a table with KO numbers. Œs it possible to retrieve information about the abundance of the differential pathways? Because I have only KO numbers in my table (without all the kegg identification levels), so I don't know how to collapse them to pathways and find out how abundant is a specific pathway in each sample.

Thanks

Francesca

gage pathways kegg • 1.2k views
0
Entering edit mode
Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 10 months ago
United States
If you want the summary expression perturbation for each pathway in each sample, you can check the stats element of the gage analysis results. Following the example in the main gage tutorial, you can do: … > gse16873.kegg.p <- gage(gse16873, gsets = kegg.gs, + ref = hn, samp = dcis) > names(gse16873.kegg.p) [1] "greater" "less" "stats" > head(gse16873.kegg.p$stats) …(a matrix with pathway as rows and samples as columns) > str(gse16873.kegg.p$stats) … HTHs, Weijun
0
Entering edit mode
Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 10 months ago
United States
If you want the summary expression perturbation for each pathway in each sample, you can check the stats element of the gage analysis results. Following the example in the main gage tutorial, you can do: … > gse16873.kegg.p <- gage(gse16873, gsets = kegg.gs, + ref = hn, samp = dcis) > names(gse16873.kegg.p) [1] "greater" "less" "stats" > head(gse16873.kegg.p$stats) …(a matrix with pathway as rows and samples as columns) > str(gse16873.kegg.p$stats) … HTHs, Weijun -------------------------------------------- On Fri, 2/27/15, francesca.defilippis [bioc] <noreply@bioconductor.org> wrote: Subject: [bioc] retrieve kegg pathway abundances from gage analysis To: luo_weijun@yahoo.com Date: Friday, February 27, 2015, 11:32 AM Activity on a post you are following on support.bioconductor.org User francesca.defilippis wrote Question: retrieve kegg pathway abundances from gage analysis: Hi! I used gage in order to perform a pathway enrichment analysis, using a table with KO numbers. Œs it possible to retrieve information about the abundance of the differential pathways? Because I have only KO numbers in my table (without all the kegg identification levels), so I don't know how to collapse them to pathways and find out how abundant is a specific pathway in each sample. Thanks Francesca You may reply via email or visit retrieve kegg pathway abundances from gage analysis