I tried to retrieve ensembl_gene_id and go_term for my arabidopsis thaliana gene from my gene_name list: > head(gene_name) gene_short_name 1 ANAC001 2 DCL1 3 MIR838A 4 AT1G01073 5 IQD18 6 AT1G01115 > unimart = useMart("plants_mart_20",dataset="athaliana_eg_gene") > getBM(attributes=c("ensembl_gene_id", "go_accession"),filters=c("ens embl_gene_id"),values=gene_name,mart=unimart) but got the folloeing error? I did not figure it out? is it an error from my side or from the biomart server? -- output of sessionInfo(): Error in getBM(attributes = c("ensembl_gene_id", "go_accession"), filters = c("ensembl_gene_id"), : Query ERROR: caught BioMart::Exception: non-BioMart die(): not well-formed (invalid token) at line 1, column 21728, byte 21728 at /usr/lib/perl5/XML/Parser.pm line 187 -- Sent via the guest posting facility at bioconductor.org.

----- Original Message ----- > From: "Waqasuddin Khan [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, waqasuddin at picb.ac.cn > Sent: Friday, January 24, 2014 6:42:06 PM > Subject: [BioC] non-BiomaRt die > > > I tried to retrieve ensembl_gene_id and go_term for my arabidopsis > thaliana gene from my gene_name list: > > head(gene_name) > gene_short_name > 1 ANAC001 > 2 DCL1 > 3 MIR838A > 4 AT1G01073 > 5 IQD18 > 6 AT1G01115 > > > unimart = useMart("plants_mart_20",dataset="athaliana_eg_gene") > > > getBM(attributes=c("ensembl_gene_id", > > "go_accession"),filters=c("ensembl_gene_id"),values=gene_name,mart =unimart) > > but got the folloeing error? I did not figure it out? is it an error > from my side or from the biomart server? > > -- output of sessionInfo(): > > Error in getBM(attributes = c("ensembl_gene_id", "go_accession"), > filters = c("ensembl_gene_id"), : > Query ERROR: caught BioMart::Exception: non-BioMart die(): > not well-formed (invalid token) at line 1, column 21728, byte 21728 > at /usr/lib/perl5/XML/Parser.pm line 187 > This error is happening on the server side. I know this because this is a perl error and there is no perl on the client side. The question is why it is happening. My guess is there is an invalid item in your gene_name vector. It could be a blank line, or something that's too long, or invalid characters. Things to try: tools::showNonASCII(gene_name) # non-ascii characters? max(nchar(gene_name)) # length of the longest gene name which(nchar(gene_name)==0) # which lines are blank? Dan > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >