Hi David,

Querying them all at once would indeed be the most efficient way to do it.
However if you have a slow internet connection you might want to split it up
in three batches or so.

Cheers,
Steffen

On Fri, Jun 11, 2010 at 2:43 PM, David Lyon <david_lyon3@yahoo.com> wrote:

> HI James
>
> That works, Thank you very much.
>
> On last question, if I wanted to map the entire human chip onto the mouse
> ship not just a few probe ids but all probes what would be the most
> efficient way of doing this?
>
> Thanks again
>
>
>
> ----- Original Message ----
> From: James W. MacDonald <jmacdon@med.umich.edu>
> To: David Lyon <david_lyon3@yahoo.com>
> Cc: Bioconductor@stat.math.ethz.ch
> Sent: Fri, June 11, 2010 5:06:02 PM
> Subject: Re: [BioC] biomaRt
>
> Hi David,
>
> David Lyon wrote:
> > Does anyone know how to map the affy probe set chips
> >
> > Human Gene 1.0 ST Array
> > to the Mouse Gene 1.0 ST Array
> >
> > using biomaRt ?
>
> > library(biomaRt)
> > human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> Checking attributes ... ok
> Checking filters ... ok
> > mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
> Checking attributes ... ok
> Checking filters ... ok
> ## get some random probeset IDs
> > library(hugene10stprobeset.db)
> > ids <- head(Lkeys(hugene10stprobesetENTREZID))
> > ids
> [1] "7892501" "7892502" "7892503" "7892504" "7892505" "7892506"
>
> > getLDS(attributes=c("hgnc_symbol", "affy_hugene_1_0_st_v1"), filters =
> "affy_hugene_1_0_st_v1", values = ids, mart = human, attributesL =
> c("mgi_symbol", "affy_mogene_1_0_st_v1"), martL = mouse)
>         V1      V2     V3       V4
> 1  SNORD58B 7892501        10600884
> 2  SNORD58B 7892501        10604240
> 3  SNORD58B 7892501        10564563
> 4  SNORD58B 7892501        10346808
> 5  SNORD58B 7892501        10356778
> 6  SNORD58B 7892501        10380670
> 7  SNORD58B 7892501        10396059
> 8  SNORD58B 7892501        10455210
> 9  SNORD58B 7892501        10405626
> 10 SNORD58B 7892501        10416835
> 11 SNORD58B 7892501        10537244
> 12 SNORD58B 7892501        10513737
> 13 SNORD58B 7892501        10552242
> 14 SNORD58B 7892501        10429389
> 15 SNORD58B 7892501        10594986
> 16 SNORD58B 7892501        10528478
> 17 SNORD58B 7892501        10456709
> 18    RPL17 7892501        10600884
> 19    RPL17 7892501        10604240
> 20    RPL17 7892501        10564563
> 21    RPL17 7892501        10346808
> 22    RPL17 7892501        10356778
> 23    RPL17 7892501        10380670
> 24    RPL17 7892501        10396059
> 25    RPL17 7892501        10455210
> 26    RPL17 7892501        10405626
> 27    RPL17 7892501        10416835
> 28    RPL17 7892501        10537244
> 29    RPL17 7892501        10513737
> 30    RPL17 7892501        10552242
> 31    RPL17 7892501        10429389
> 32    RPL17 7892501        10594986
> 33    RPL17 7892501        10528478
> 34    RPL17 7892501        10456709
> 35   TARDBP 7892506 Tardbp 10518532
> 36   TARDBP 7892506 Tardbp       NA
>
> Best,
>
> Jim
>
>
>
> >
> > Thanks
> >
> > _______________________________________________
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>
> -- James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
> 5912 Buhl
> 1241 E. Catherine St.
> Ann Arbor MI 48109-5618
> 734-615-7826
> **********************************************************
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