[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?



> 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) 

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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