Dear Hans,

thank you very much for your feedback. Now everything is working!

best
r

On 6 September 2010 12:20, Hans-Rudolf Hotz <hrh@fmi.ch> wrote:

> René
>
> Have you tried again in the meantime, as this looks more like a temporary
> glitch on the biomart backend?
>
> ie it works form me:
>
>
> > library("biomaRt")
> > mart = useMart("ensembl")
> > ensembl = useDataset("hsapiens_gene_ensembl", mart=mart)
> Checking attributes ... ok
> Checking filters ... ok
> > EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102")
> > utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl,
> type="entrezgene")
> >
> > utr['entrezgene']
>  entrezgene
> 1         25
> 2        102
> 3         25
> 4         87
> >
>
> (although, I am not quite sure, what you are trying to fetch from biomart)
>
>
> regards, Hans
>
>
>
>
> > sessionInfo()
> R version 2.11.1 (2010-05-31)
> x86_64-unknown-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] biomaRt_2.4.0
>
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.4-3 XML_3.1-1
>
> >
>
>
>
>
> On 09/06/2010 10:58 AM, René Dreos wrote:
>
>> Dear BioC mailing-list,
>>
>> I came across this error using the latest R version and BioMart:
>>
>>  library("biomaRt")
>>> mart = useMart("ensembl")
>>> ensembl = useDataset("hsapiens_gene_ensembl", mart=mart)
>>>
>> Checking attributes ... ok
>> Checking filters ... ok
>>
>>> EGsub = c("1635_at"="25", "39329_at"="87", "40797_at"="102")
>>> utr = getSequence(id=EGsub, seqType="3utr", mart=ensembl,
>>>
>> type="entrezgene")
>>
>>                                                  V1
>> 1<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01
>> Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
>> 2<HTML><HEAD><META
>> HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1">
>> 3
>> <TITLE>ERROR: The requested URL could not be retrieved</TITLE>
>> 4<STYLE
>>
>> type="text/css"><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
>> 5
>>                                        </HEAD><BODY>
>> 6
>>                                       <H1>ERROR</H1>
>> Error in getBM(c(seqType, type), filters = type, values = id, mart = mart,
>>  :
>>   The query to the BioMart webservice returned an invalid result: the
>> number
>> of columns in the result table does not equal the number of attributes in
>> the query. Please report this to the mailing list.
>>
>> I looked through the BioC mailing-list for similar errors but found only
>> one
>> quite similar last year. It was related to a bug in BioMart. Is this the
>> same?
>>
>> Here is my session-info:
>>
>>> sessionInfo()
>>>
>> R version 2.11.1 (2010-05-31)
>> x86_64-apple-darwin9.8.0
>>
>> locale:
>> [1] C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>  [1] RCurl_1.4-2
>>  [2] bitops_1.0-4.1
>>  [3] ChIPpeakAnno_1.4.1
>>  [4] limma_3.4.4
>>  [5] org.Hs.eg.db_2.4.1
>>  [6] GO.db_2.4.1
>>  [7] RSQLite_0.9-2
>>  [8] DBI_0.2-5
>>  [9] AnnotationDbi_1.10.2
>> [10] BSgenome.Ecoli.NCBI.20080805_1.3.16
>> [11] multtest_2.5.14
>> [12] Biobase_2.8.0
>> [13] biomaRt_2.4.0
>> [14] chipseq_0.4.1
>> [15] ShortRead_1.6.2
>> [16] Rsamtools_1.0.8
>> [17] lattice_0.18-8
>> [18] BSgenome.Athaliana.TAIR.04232008_1.3.16
>> [19] BSgenome_1.16.5
>> [20] Biostrings_2.16.9
>> [21] GenomicRanges_1.0.8
>> [22] IRanges_1.6.15
>>
>> loaded via a namespace (and not attached):
>> [1] MASS_7.3-6      XML_3.1-1       grid_2.11.1     hwriter_1.2
>> [5] splines_2.11.1  survival_2.35-8 tcltk_2.11.1    tools_2.11.1
>>
>>
>> Thank you very much for any feed-back,
>>
>> best
>> r
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>

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