[BioC] BioMart error

Mon Sep 6 13:20:32 CEST 2010

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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