[BioC] From KEGG pathways to Affy ProbeID

[John Zhang]

>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)?


>library(rgu34a)
>library(KEGG)
>rat34a <- as.list(rgu34aPATH2ID)
>names(rat34a) <- unlist(mget(names(rat34a), KEGGPATHID2NAME))
>rat34a[1]
$"Propanoate metabolism"
[1] "J03621_at"		"U75393_s_at"		"AB004329_at" ...
...



>
>Thank you very much in advance.
>
>Regards,
>Sharon
>
>	[[alternative HTML version deleted]]
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084