Search
Question: biomart error returning data
0
gravatar for Guest User
6.3 years ago by
Guest User12k
Guest User12k wrote:
Hello I ran the below commands and got an error. The output asked me to post to the list so here it is. a similar problem was reported for a different related database query: http://article.gmane.org/gmane.science.biology.informatics.conductor/2 5233/match=biomart+invalid+result I will go about it in an different way I think thanks Alasdair -- output of sessionInfo(): > M1_0.exprs = read.table("M1_0.txt", sep="\t", header=TRUE) > library(biomaRt) > ensembl.mart = useMart(biomart="ensembl",dataset="mmusculus_gene_ensembl") > ensembl.gene.pos = getBM(attributes = c("ensembl_gene_id","chromosom e_name","start_position","end_position"), filters = "ensembl_gene_id", values = rownames(M1_0.exprs), mart = ensembl.mart) V1 1 2 <html><head><meta http-="" equiv="Content-Type" content="text/html;" charset="iso-8859-1"> 3 ERROR: The requested URL could not be retrieved 4 <style type="text/css"></style> 5 </head><body> 6

ERROR

Error in getBM(attributes = c("ensembl_gene_id", "chromosome_name", "start_position", : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list. > sessionInfo() R version 2.15.0 (2012-03-30) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] biomaRt_2.12.0 loaded via a namespace (and not attached): [1] RCurl_1.91-1 tools_2.15.0 XML_3.9-4 > traceback() 2: stop("The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.") 1: getBM(attributes = c("ensembl_gene_id", "chromosome_name", "start_position", "end_position"), filters = "ensembl_gene_id", values = rownames(data), mart = ensembl.mart) -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink written 6.3 years ago by Guest User12k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 134 users visited in the last hour