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Dear Marco, Thank you for reporting this. This is a bug, the large number 2500000000 gets replaced in R by 2.5e+09 which is not understood by the webservice at the Ensembl end. Try putting the number between quotes so it doesn't get converted in R and your query should work. gene.list <- getFeature(chromosome=1,start=0,end="2500000000",type="entrezgene", mart=ensmart) Cheers, Steffen -----Original Message----- From: marco zucchelli [mailto:marco.bioc@gmail.com] Sent: Mon 6/18/2007 7:29 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] changes in biomart database ? Dear all, the following piece of code worked until friday to get the genes with entrez ID on chr1. ## library(biomaRt) ensmart <- useMart("ensembl",dataset="hsapiens_gene_ensembl") gene.list <- getFeature(chromosome=1,start=0,end=2500000000,type="entrezgene", mart=ensmar > gene.list NULL ## today the "gene.list" is NULL. Is there any change going on in the biomart database ? R version 2.5.0 (2007-04-23) 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" "datasets" "utils" "methods" [7] "base" other attached packages: biomaRt RCurl XML "1.10.0" "0.8-0" "1.9-0" Marco [[alternative HTML version deleted]] _______________________________________________ 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