On Mon, Apr 14, 2008 at 9:17 AM, Gonzalo G?mez <ggomez at="" cnio.es=""> wrote: > Hi Sean, I dont know if there?s something wrong in the getGene function. > The same code that you sent me does not work in my computer...and the data > type proposed does not work... > > Thanks again > > G > > This is the code: > > > library(biomaRt) > Loading required package: XML > Loading required package: RCurl > > > ensembl = useMart("ensembl", dataset = "mmusculus_gene_ensembl") > Checking attributes and filters ... ok > > > AgiIDs<- c("A_51_P227502","A_52_P330395","A_51_P183051") > > > Agilent<-getGene(AgiIDs, type = 'agilent_probe', mart=ensembl) > Error in mapFilter(type) : invalid type choose either affy, refseq, embl, > hugo, ensembl, ensemblTrans, unigene, agilentprobe or entrezgene > > > Agilent<-getGene(AgiIDs, type = 'agilentprobe', mart=ensembl) > Error in getBM(attributes = c(filter, symbol, "description", chrname, : > Invalid attribute(s): agilentprobe > Please use the function 'listAttributes' to get valid attribute names > > > sessionInfo() > R version 2.4.1 (2006-12-18) > i386-apple-darwin8.8.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" > "base" > other attached packages: > biomaRt RCurl XML > "1.8.2" "0.8-0" "1.7-2" Hi, Gonzalo. It would be helpful to always write to the bioconductor list with questions. First, there are people who use biomaRt much more that I do that read and answer the list. In addition, everyone then gets the benefit of the exchange. As you can see below, this works fine for me. Since you included your sessionInfo(), I see that you are using a version of R that is about 2-1/2 years out-of-date and that your biomaRt is very old, also. I would suggest upgrading your R to the most recent release, installing biomaRt, and then trying your query again. Sean > library(biomaRt) Loading required package: RCurl > ensembl = useMart("ensembl", dataset = "mmusculus_gene_ensembl") Checking attributes and filters ... ok > AgiIDs<- c("A_51_P227502","A_52_P330395","A_51_P183051") > Agilent<-getGene(AgiIDs, type = 'agilent_probe', mart=ensembl) > Agilent agilent_probe mgi_symbol 1 A_51_P183051 Upb1 2 A_51_P227502 Mfap2 3 A_52_P330395 Farp1 description 1 Beta-ureidopropionase (EC 3.5.1.6) (Beta-alanine synthase) (N- carbamoyl-beta-alanine amidohydrolase). [Source:Uniprot/SWISSPROT;Acc:Q8VC97] 2 Microfibrillar-associated protein 2 precursor (MFAP-2) (Microfibril- associated glycoprotein) (MAGP) (MAGP-1). [Source:Uniprot/SWISSPROT;Acc:P55002] 3 FERMRhoGEF (Arhgef) and pleckstrin domain protein 1 [Source:RefSeq_peptide;Acc:NP_598843] chromosome_name band strand start_position end_position ensembl_gene_id 1 10 B5.3 1 74869760 74904424 ENSMUSG00000033427 2 4 D3 1 140566596 140571882 ENSMUSG00000060572 3 14 E4 1 121434766 121682948 ENSMUSG00000025555 > sessionInfo() R version 2.7.0 Under development (unstable) (2008-01-15 r44010) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_1.13.10 RCurl_0.8-3 loaded via a namespace (and not attached): [1] XML_1.93-2