[BioC] Mapping GO term ID to Illumina probe ID for Illumina gene expression data

[Pan Du]

Hi Allen,

The GOID should include "GO:" before the numeric number.

> library(lumi)
> library(lumiHumanAll.db)
> m <- mget("GO:0043473",lumiHumanAllGO2PROBE,ifnotfound = NA)
> m

The returns are corresponding Illumina probes (identified by nuIDs) included
in all types of Illumina Human chips. If you want to know the original
Illumina probe IDs, you can use the following code:

> illuminaProbeID <- nuID2IlluminaID(m[[1]], lib.mapping='lumiHumanIDMapping',
idType='Probe')

Because function "nuID2IlluminaID" only returns the matched probe
information within the best matched chip type, some input IDs included in
other types of chips will not be matched. So if you see the warning message
"Some input IDs can not be matched!", it is fine. You can just remove the
Nas.



Pan




On 2/24/09 5:00 AM, "bioconductor-request at stat.math.ethz.ch"
<bioconductor-request at stat.math.ethz.ch> wrote:

> Date: Mon, 23 Feb 2009 22:38:33 -0500
> From: ss <affysnp at gmail.com>
> Subject: [BioC] Mapping GO term ID to Illumina probe ID for Illumina
> gene expression data
> To: BioC <bioconductor at stat.math.ethz.ch>
> Message-ID:
> <5032046e0902231938m777dbad2h3dc337b9df8afd2b at mail.gmail.com>
> Content-Type: text/plain
> 
> Hi all,
> 
> I am trying to map a GO term (GO:0043473) which I am interested
> to Illumina probe ID. This GO term is available at:
> http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:0043473&s
> ession_id=7969amigo1235444600
> 
> 
> The code I have tried so far is:
> 
>> library(lumi)
>> library(lumiHumanAll.db)
>> m<-mget("0043473",lumiHumanAllGO2PROBE,ifnotfound = NA)
>> m
> $`0043473`
> [1] NA
> 
> It is weird that I end up with nothing. I did try lumiHumanAllGO2ALLPROBES
> though, but no luck.
> 
>> m<-mget("0043473",lumiHumanAllGO2ALLPROBES,ifnotfound = NA)
>> m
> $`0043473`
> [1] NA
> 
> Interestingly enough, I had no problem with mapping KEGG ID to probe ID
> by using "lumiHumanAllPATH2PROBE".
> 
> If anybody can help me figure it out, that will be greatly appreciated.
> Have a good one.
> 
> Allen
> 
> [[alternative HTML version deleted]]
> 
> 
> 


------------------------------------------------------
Pan Du, PhD
Research Assistant Professor
Northwestern University Biomedical Informatics Center
750 N. Lake Shore Drive, 11-176
Chicago, IL  60611
Office (312) 503-2360; Fax: (312) 503-5388
dupan (at) northwestern.edu