Unclear error in getBM() with attributes and output
0
0
Entering edit mode
@krispetrini-7786
Last seen 4.5 years ago
Italy

Hi!

I'm trying to use the function getBM(), but I have some unclear problems with this function:

this is my simple script:

library("biomaRt")
agilent_ID<-scan("/home/cristiano/kris/Scrivania/Temporanei_tirocinio/R/Agilent ID spot.csv", ,what="character",skip=1,quiet=TRUE)[1]
oldmouse<-useMart(biomart="ENSEMBL_MART_ENSEMBL", host="may2012.archive.ensembl.org", path="/biomart/martservice",dataset ="mmusculus_gene_ensembl")
annot <- c("ensembl_gene_id", "external_gene_id", "start_position", "strand", "gene_flank", "5utr", "3utr", "3_utr_start", "5_utr_start", "description", "gene_exon_intron" , "gene_exon")
filt <- "efg_agilent_wholegenome_4x44k_v1"
tutto <- getBM(annot, filt, agilent_ID, oldmouse)
write(tutto, "tutto.f)

when I use it I have this error:

Error in getBM(annot, filt, agilent_ID, oldmouse) : 
  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.
 
getBM software error • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 798 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6