Thanks Steffen and James for your help....have a good weekend. Cheers ________________________________ From: Steffen Durinck Cc: James W. MacDonald ; Bioconductor@stat.math.ethz.ch Sent: Fri, June 11, 2010 6:10:43 PM Subject: Re: [BioC] biomaRt 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 >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 >>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 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@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 > >>_______________________________________________ >>Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]