[BioC] changes in biomart database ?

[Durinck, Steffen (NIH/NCI) [F]]

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 at 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