Hi James, This is probably due to a change in the VEGA BioMart database and I will check this out. You should be able to use Ensembl though to get gene information from entrezgene identifiers using quotes or not. Try the following: > mart=martConnect() connected to: ensembl_mart_35 > getGene(id=100, type="entrezgene", species="hsapiens", mart=mart) id symbol 1 100 ADA description 1 Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase). [Source:Uniprot/SWISSPROT;Acc:P00813] band chromosome start end strand martID 1 q13.12 20 42681578 42713790 -1 ENSG00000196839 > getGene(id="100", type="entrezgene", species="hsapiens", mart=mart) id symbol 1 100 ADA description 1 Adenosine deaminase (EC 3.5.4.4) (Adenosine aminohydrolase). [Source:Uniprot/SWISSPROT;Acc:P00813] band chromosome start end strand martID 1 q13.12 20 42681578 42713790 -1 ENSG00000196839 I get an error when I run the example for getGene in the biomaRt package on both windows and linux. It appears that the martTable class expects the id to be character, but for e.g. Entrez Gene the id is numeric. If I substitute id="100", I get a martTable, but with all NA for all slots but the id. >> example(getGene) getGen> if (interactive()) { mart <- martConnect(biomarts = c("ensembl", "vega")) g = getGene(id = "1939_at", array = "hg_u95av2", mart = mart) show(g) g = getGene(id = 100, type = "entrezgene", species = "hsapiens", db = "vega", mar .... [TRUNCATED] connected to: ensembl_mart_35 connected to: vega_mart_35 An object of class "martTable" Slot "id": [1] "1939_at" Slot "table": $symbol [1] "TP53" $description [1] "Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein p53) (Antigen NY-CO-13). [Source:Uniprot/SWISSPROT;Acc:P04637]" $band [1] "p13.1" $chromosome [1] "17" $start [1] 7512464 $end [1] 7531642 $martID [1] "ENSG00000141510" Error in validObject(.Object) : invalid class "martTable" object: invalid object for slot "id" in class "martTable": got class "numeric", should be or extend class "character" >> sessionInfo() R version 2.2.0, 2005-10-12, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" "datasets" [8] "base" other attached packages: biomaRt XML RMySQL DBI hs133phsug6cdf affy "1.4.0" "0.97-0" "0.5-6" "0.1-9" "6.0.0" "1.8.1" Biobase "1.7.4" Any ideas? Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** 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 at stat.math.ethz.ch htt Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm