[Bioc-devel] <no subject>

[Wolfgang Huber]

Dear Julie

I ran the code below and it worked fine for me. If you want help, can 
you try being more precise than "sometimes produces error but sometimes 
not" - e.g. exactly specify the sessionInfo() and the code you run in 
both cases, and the time and date?

There could be a multitude of reasons, which we need to exclude step by 
step, such as your using different versions of R and its packages, 
different BioMart servers, different types of internet connection. I 
would not be surprised if your problem were a biomaRt package version issue.

	Best wishes
	Wolfgang

PS - Your code example contained a typo and could not have worked 
(uppercase "L" in the "library" function). Please be sure to always 
report precisely what you're doing and don't assume small details don't 
matter.


  library(biomaRt)
  mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
  seq1 = getSequence(id = "ENSDARG00000054562",
              type = "ensembl_gene_id", seqType = "gene_exon_intron",
               upstream = 350, mart = mart)
  seq1
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
                                                  gene_exon_intron
1 GTGTCTTTTCCCTCCCCTGGGAAATGATCGTATGTCTACAGTCTCCATCT....
      ensembl_gene_id
1 ENSDARG00000054562

 > sessionInfo()
R version 2.10.0 Under development (unstable) (2009-06-12 r48755)
x86_64-unknown-linux-gnu

locale:
  [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=it_IT.UTF-8        LC_COLLATE=it_IT.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=it_IT.UTF-8
  [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] biomaRt_2.1.0  fortunes_1.3-6

loaded via a namespace (and not attached):
[1] RCurl_0.98-1 XML_2.5-1



> Dear BiomaRt developers,
> 
> The following code using biomaRt sometimes produces error but sometimes not.
> Could you please help me to resolve the issue? Thanks a lot for your help!
> 
> Library(biomaRt)
> mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
> seq1 = getSequence(id = "ENSDARG00000054562",
>             type = "ensembl_gene_id", seqType = "gene_exon_intron",
>              upstream = 350, mart = mart)
> Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"),  :
>>   Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
>> FOUND
> 
> FYI, this error also occurs in the development version of R.
>  
> Best regards,
> 
> Julie
> 
>  sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
> 
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] biomaRt_2.0.0
> 
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 XML_2.3-0
> 
> _______________________________________________
> Bioc-devel at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 

Best wishes
      Wolfgang

------------------------------------------------
Wolfgang Huber, EMBL, http://www.ebi.ac.uk/huber