[BioC] biomaRt:getBM error when query is large
Shi, Tao
shidaxia at yahoo.com
Fri Aug 1 23:34:45 CEST 2008
Hi list,
See the sample codes below, where "rs" is a char vector containing ~430000 rs IDs. However, when I ran the query 10000 at a time, it worked. Is there a query limit for biomaRt?
Thanks,
...Tao
> tmp <- getBM(c("ensembl_gene_stable_id", "refsnp_id", "allele", "chr_name", "chrom_start", "chrom_strand"),
+ filters = "refsnp", values = rs, mart = mart)
Error in postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery) :
Empty reply from server
> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-mingw32
locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
attached base packages:
[1] tools stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_1.14.0 RCurl_0.9-3 GO.db_2.2.0 AnnotationDbi_1.2.2 RSQLite_0.6-9 DBI_0.2-4 Biobase_2.0.1
loaded via a namespace (and not attached):
[1] XML_1.95-2
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