[Bioc-devel] biomaRt help
Julie Zhu
julie.zhu at umassmed.edu
Tue Jun 16 14:24:45 CEST 2009
Dear Wolfgang,
Thank you very much for trying to reproduce the error and trying to fix!
Best regards,
Julie
On 6/16/09 7:57 AM, "Wolfgang Huber" <huber at ebi.ac.uk> wrote:
>
> Dear Julie,
>
> thanks for reporting this. I have tried your code
>
> 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)
>
> and reproduced the error:
>
> Errore in getBM(c(seqType, type), filters = c(type, "upstream_flank"),:
> Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
> FOUND
>
> both on
>
> R 2.9.0 with biomaRt_2.0.0, RCurl_0.98-1, XML_2.5-1
>
> and
>
> R 2.10.0 with biomaRt_2.1.0, RCurl_0.98-1, XML_2.5-1
>
> We will investigate.
>
> Thanks
> Wolfgang
>
>
>
>
> Julie Zhu ha scritto:
>> 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
>>
>> _______________________________________________
>> Bioc-devel at stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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