[BioC] biomaRt error

[Iain Gallagher]

Seems to be ok this morning. Ran the same query with no problems. Perhaps some transient changes at the server end.

Cheers

Iain

--- On Wed, 13/1/10, Paul Leo <p.leo at uq.edu.au> wrote:

> From: Paul Leo <p.leo at uq.edu.au>
> Subject: Re: [BioC] biomaRt error
> To: "Iain Gallagher" <iaingallagher at btopenworld.com>
> Cc: bioconductor at stat.math.ethz.ch
> Date: Wednesday, 13 January, 2010, 23:45
> Dito.
> Actually 3 days ago some of my old queries started
> returning different
> numbers of rows 
> 
> 
> length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding"
> ,
> "ensembl_gene_id"]))
> [1] 19940
> 
> >
> length(unique(ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="protein_coding"
> , "ensembl_gene_id"])) # 22836
> [1] 22836
> 
> vs for months before hand and 4 days previous
> 
> length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding"
> ,
> "ensembl_gene_id"])) 
> [1] 22836
> 
> >
> length(unique(ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="protein_coding"
> , "ensembl_gene_id"])) # 22836
> [1] 22836
> 
> FOR
> a.filter<-c( "chromosome_name", "start" , "end")
> fil.vals<-list(chrom,  low.cut, high.cut)
> 
> ann.all<-getBM(attributes =
> c("ensembl_gene_id","external_gene_id","chromosome_name","start_position","end_position","strand","gene_biotype","mgi_symbol","description"),
> filters = a.filter, values=fil.vals, mart = mart)
> 
> ann.all.entrez<-getBM(attributes =
> c(
> "ensembl_gene_id","external_gene_id","ensembl_transcript_id","chromosome_name","start_position","end_position","strand","gene_biotype","entrezgene","mgi_symbol","description"),
> filters = a.filter, values=fil.vals, mart = mart)
> 
> No idea why the first query was affected and not the
> second.... This did
> coincide with a bioC update I did two days ago... but that
> may be a
> coincidence....
> 
> 
> 
> 
> Today I get the same error
> > listMarts()
> Error: non-BioMart die(): 
> not well-formed (invalid token) at line 1, column 11797,
> byte 11797
> at /usr/lib/perl5/XML/Parser.pm line 187
> 
>   does not seem to be XML, nor to identify a file
> name
> 
> 
> 
> 
> > sessionInfo()
> R version 2.10.1 (2009-12-14) 
> x86_64-pc-linux-gnu 
> 
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8   
>    LC_NUMERIC=C       
>       
>  [3] LC_TIME=en_AU.UTF-8       
> LC_COLLATE=en_AU.UTF-8    
>  [5] LC_MONETARY=C           
>   LC_MESSAGES=en_AU.UTF-8   
>  [7] LC_PAPER=en_AU.UTF-8   
>    LC_NAME=C       
>          
>  [9] LC_ADDRESS=C           
>    LC_TELEPHONE=C       
>     
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C 
>      
> 
> attached base packages:
> [1] stats     graphics  grDevices
> utils     datasets  methods
> base     
> 
> other attached packages:
> [1] org.Mm.eg.db_2.3.6  RSQLite_0.8-1   
>    DBI_0.2-5       
>   
> [4] AnnotationDbi_1.8.1 Biobase_2.6.1   
>    biomaRt_2.2.0      
> 
> loaded via a namespace (and not attached):
> [1] RCurl_1.3-1  tcltk_2.10.1 tools_2.10.1
> XML_2.6-0  
> 
> 
> 
> -----Original Message-----
> From: Iain Gallagher <iaingallagher at btopenworld.com>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] biomaRt error
> Date: Wed, 13 Jan 2010 19:00:14 +0000 (GMT)
> 
> Hello List
> 
> Can anyone shed any light on the following biomaRt error?
> Has something changed at Ensembl?
> 
> > library(biomaRt)
> > 
> > mart <- useMart("ensembl",
> dataset="hsapiens_gene_ensembl")
> Error: non-BioMart die(): 
> not well-formed (invalid token) at line 1, column 11797,
> byte 11797 at /usr/lib/perl5/XML/Parser.pm line 187
> 
>   does not seem to be XML, nor to identify a file
> name
> > sessionInfo()
> R version 2.10.1 (2009-12-14) 
> x86_64-pc-linux-gnu 
> 
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8   
>    LC_NUMERIC=C       
>       
>  [3] LC_TIME=en_GB.UTF-8       
> LC_COLLATE=en_GB.UTF-8    
>  [5] LC_MONETARY=C           
>   LC_MESSAGES=en_GB.UTF-8   
>  [7] LC_PAPER=en_GB.UTF-8   
>    LC_NAME=C       
>          
>  [9] LC_ADDRESS=C           
>    LC_TELEPHONE=C       
>     
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C 
>      
> 
> attached base packages:
> [1] stats     graphics  grDevices
> utils     datasets 
> methods   base     
> 
> other attached packages:
> [1] biomaRt_2.2.0
> 
> loaded via a namespace (and not attached):
> [1] RCurl_1.3-1 XML_2.6-0  
> > 
> 
> Thanks
> 
> Iain
> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
>