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Old 03-14-2014, 06:07 PM   #28
bigmw
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Your original code worked well in this step as show in your reponse #24 above.
> gnames.eg=pathview::id2eg(gnames, category ="symbol", org="Ss")
Loading required package: org.Ss.eg.db

This line above had no problem. Changing org= "Ss" to "Ssc" and "ssc" caused all the errors. There is no way you will get the input of org="Ss" and message with org.ssc.eg.db like below:
>gnames.eg=pathview::id2eg(gnames, category ="symbol", org="Ss")
Loading required package: org.ssc.eg.db


Quote:
Originally Posted by shocker8786 View Post
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.
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