Question: master gene list for pathway analysis
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gravatar for maria
12 months ago by
maria0
maria0 wrote:

I’d like to conduct a pathway analysis using the bioconductor package sigPathway (bioconductor version 3.7.). In the vignette, there is a link to a master gene list (Genesets_EntrezGeneIDs.RData). As the link cannot be opened (Error: Page not found), I downloaded the RData-File from the homepage http://compbio.med.harvard.edu/Supplements/PNAS05.html. The homepage was last modified at December 5, 2005, so I wonder if I can still use this master gene list?  Or do I have to create my own master gene list? Which bioconductor package/ -functions do you recommend for creating a master gene list (I’m working with Affymetrix hugene 2.1st, the annotation package I used to get the Entrez-IDs is hugene21sttranscriptcluster.db).

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