Question: Unclear error in getBM() with attributes and output
0
gravatar for kris.petrini
4.4 years ago by
Italy
kris.petrini0 wrote:

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.
 
software error getbm • 569 views
ADD COMMENTlink written 4.4 years ago by kris.petrini0
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