View Single Post
Old 03-14-2014, 02:29 AM   #26
shocker8786
Member
 
Location: Urbana Illinois

Join Date: Jan 2013
Posts: 28
Default

I think you are right, but I'm not sure how exactly to download the pathway data files. I thought the step you told me to change (below) would download the package I need, but it fails:

gnames.eg=pathview::id2eg(gnames, category ="symbol", org="Ss")
Loading required package: org.ssc.eg.db
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.3.
Installing package(s) 'org.Ss.eg.db'
Loading required package: org.Ss.eg.db
Error in pathview::id2eg(gnames, category = "symbol", org = "Ss") :
Fail to install/load gene annotation package org.Ss.eg.db!
In addition: Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘org.Ss.eg.db’
2: package ‘org.ssc.eg.db’ is not available (for R version 3.0.3)
3: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘org.Ss.eg.db’

I changed org= "Ss" to "Ssc" and "ssc", but the result is the same, there does not seem to be a database with this name. However on the KEGG website, pig is listed as ssc. Is this the proper way to download the database, or is there another step I am missing? Thanks.
shocker8786 is offline   Reply With Quote