[Bioc-devel] biomaRt help

[Julie Zhu]

Dear Wolfgang,

Thank you very much for trying the code and pointing out the typo!

I just tried the code again three times. The getBM call produced the error
on the first and third time, but on the second time the getBM call works
fine. Here is the code I ran and the output including time, date and session
information.

Best regards,

Julie

> library(biomaRt)
> mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
> date()
[1] "Mon Jun 15 08:35:19 2009"
> 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

> 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
> library(biomaRt)
> mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok
> date()
[1] "Mon Jun 15 08:36:09 2009"
> seq1 = getSequence(id = "ENSDARG00000054562",
+             type = "ensembl_gene_id", seqType = "gene_exon_intron",
+                 upstream = 350, mart = mart)
> date()
[1] "Mon Jun 15 08:36:39 2009"
> 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

> 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


On 6/14/09 4:00 AM, "Wolfgang Huber" <huber at ebi.ac.uk> wrote:

> 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
>