Thanks so much, Steffen; that answers my question perfectly.

Wyatt

K. Wyatt McMahon, Ph.D.
Postdoctoral Research Associate
Department of Internal Medicine
3601 4th St. - Lubbock, TX - 79430
P: 806-743-4072
F: 806-743-3148

From: Steffen Durinck [mailto:sdurinck@lbl.gov]
Sent: Wednesday, October 13, 2010 4:40 PM
To: Mcmahon, Kwyatt
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] omitted rows using getBM

Hi Wyatt,

Ensembl does it's own mapping of affy ids to the genome.  If they decide there is no good match for an affy probe to the genome then they won't provide any result for that probe, which explains the reduced number of rows.

Cheers,
Steffen
On Wed, Oct 13, 2010 at 2:32 PM, Mcmahon, Kwyatt <kwyatt.mcmahon@ttuhsc.edu<mailto:kwyatt.mcmahon@ttuhsc.edu>> wrote:
Hello everyone,

I'm trying to use biomaRt to simply get the Entrez Gene IDs from a list of probe ids from the Affymetrix Mouse 430 2.0 chip.  When I use the getBM function, I end up getting a different number of rows in the resulting table than I input.  I've read the getBM help and searched this mailing list, but to no avail.  My code is below:

>mart<-useMart("ensembl", dataset="mmusculus_gene_ensembl")
>genetable1239<-getBM(attributes=c("affy_mouse430_2","entrezgene"), values=gds1239[,1], filters="affy_mouse430_2", mart=mart)
>dim(gds1239)
[1] 45101     2
> dim(genetable1239)
[1] 43488     2
> length(unique(gds1239[,1]))
[1] 45101

Can anyone help me?

Thanks so much,

Wyatt

> sessionInfo()
R version 2.11.1 (2010-05-31)
i386-pc-mingw32

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GEOquery_2.13.5 Biobase_2.8.0   biomaRt_2.4.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-2  tools_2.11.1 XML_3.1-0



K. Wyatt McMahon, Ph.D.
Postdoctoral Research Associate
Department of Internal Medicine
3601 4th St. - Lubbock, TX - 79430
P: 806-743-4072
F: 806-743-3148


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