[BioC] biomaRt

[James W. MacDonald]

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
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues