[shriram]

Hi
I am using pathview for yeast however I get following error while retrieving pathway information for 19 different pathways.
[1] "Downloading xml files for sce04113 Meiosis - yeast, 1/19 pathways.."
[1] "Downloading png files for sce04113 Meiosis - yeast, 1/19 pathways.."
Download of sce04113 Meiosis - yeast xml and png files failed!
Failed to download KEGG xml/png files, sce04113 Meiosis - yeast skipped!

Same functionality works fine with human data.

below is my R version
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

Thanks
Shriram

############
Issue resolved
by taking substring of actual pathway name in kegg and specifying gene.idtype="KEGG"
path.ids <- substr(path.ids, 1, 8)
############

[shriram]

Hi
I am using pathview for yeast however I get following error while retrieving pathway information for 19 different pathways.
[1] "Downloading xml files for sce04113 Meiosis - yeast, 1/19 pathways.."
[1] "Downloading png files for sce04113 Meiosis - yeast, 1/19 pathways.."
Download of sce04113 Meiosis - yeast xml and png files failed!
Failed to download KEGG xml/png files, sce04113 Meiosis - yeast skipped!

Same functionality works fine with human data.

below is my R version
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)

Thanks
Shriram

[bigmw]

gage package has a function, kegg.gsets, to generate updated pathway gene set data in real time for ~ 2300 KEGG species and KEGG Orthology (with species="ko").
gageData package provides kegg and GO gene sets for 4 common research species: human, mouse, rat and budding yeast.
You may want to go through the main vignette and other documents of gage package (besides the RNA-Seq workflow tutorial):

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/gage.pdf

http://bioconductor.org/packages/release/bioc/html/gage.html

gageData is available:

http://bioconductor.org/packages/release/data/experiment/html/gageData.html

[wilson90]

In your vignette, we are suppose to provide our annotation file.
I wonder where have you obtained "kegg.gs"?
and I want to use GO annotation. So where can I obtain "GO.gs" in R?
Thank you.

Frustrated user

[crazyhottommy]

Thank you!

[bigmw]

If you follow the RNA-seq workflows (links in the first post above), we can actually work on the demo examples from Step 2. In other words, we can start with the pre-mapped raw read counts data (from previous steps), i.e. hnrnp.cnts stored in gageData. I would suggest you to run the demo example and explore gage/pathview functions and input/output data by yourself.

[bigmw]

You don’t have to change gene names/IDs to GO term IDs. GAGE (or other gene set analysis tools) requires two major input data objects: your expression data (vector or matrix-like) and gene set list (list of gene ID vectors). Make sure your gene IDs in expression data and gene set list are the same type, i.e. both are Entrez Gene IDs, or both gene symbols, etc.
You may want to go through the basics and common use of gage described in the main gage vignette:

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/gage.pdf

if you want a quick start, section 1, 6 and 7 (page 1, 4-8) would be enough. You will see examples for both KEGG and GO analysis.

[crazyhottommy]

Hi I was playing around with GAGE, one question is that I got the count table by HTSeq, and the ids are gene names for each row, how can I change the gene names to GO term ids?

Thanks

[bigmw]

Pathview is actually applicable to any data mappable to pathways, including gene, protein, metabolite, genetics, literature, and others. The tutorial describes examples on metabolite/compound data too.

[bigmw]

GAGE/Pathview workflow can be applied for microarray data analysis. Please check the main tutorials of gage and pathview for details:

http://bioconductor.org/packages/release/bioc/vignettes/gage/inst/doc/gage.pdf

http://bioconductor.org/packages/release/bioc/vignettes/pathview/inst/doc/pathview.pdf

[entrez]

Can I use the workflow (with necessary changes) for microarray data analysis? If so, how?

[bigmw]

If you don’t know how to upgrade Bioc, please check:

http://www.bioconductor.org/install/#update-bioconductor-packages

Here is some work around if you get problems:

https://stat.ethz.ch/pipermail/bioconductor/2013-October/055642.html

[bigmw]

pathview 1.1.4 does not show multiple samples/states in the same graph, you need to upgrade to the current release, which is 1.2.0: http://bioconductor.org/packages/rel.../pathview.html.
I would recommend to do an overall upgrade to R 3.0.2/Bioconductor 2.13, which will update your pathview and gage to the latest version too.

[entrez]

gage 2.10.0, pathview 1.1.4 and Bioconductor 2.12

[bigmw]

What versions of gage, pathview and Bioconductor you have?