[BioC] From KEGG pathways to Affy ProbeID

John Zhang jzhang at jimmy.harvard.edu
Mon Dec 5 17:19:14 CET 2005

>I am trying to get Affy ProbeID for all the pathways (particularly for
>"rat") in KEGG.  I have found a way to do this using
>contents(KEGGPATHID2NAME) environment and by using grep to match a
>particular pathway. I have to do this step manually for all the pathways. Is
>there any other ways to extract affy probeids for corresponding pathways?

Is this what you want to do (using rgu34a as an example)?

>rat34a <- as.list(rgu34aPATH2ID)
>names(rat34a) <- unlist(mget(names(rat34a), KEGGPATHID2NAME))
$"Propanoate metabolism"
[1] "J03621_at"		"U75393_s_at"		"AB004329_at" ...

>Thank you very much in advance.
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>Bioconductor at stat.math.ethz.ch

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

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