[BioC] biomart error

Natasha Sahgal nsahgal at well.ox.ac.uk
Thu Aug 18 18:54:14 CEST 2011 

Dear Herve,

Thanks for this.

Though with "with_illumina_humanht_12" and "illumina_humanht_12"  are 
definitely in the filters.

listMarts(host="www.ensembl.org")
ensembl =  useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", 
dataset="hsapiens_gene_ensembl")
filt = listFilters(ensembl)

filt[grep("illumina", filt[[1]], ignore.case=TRUE), ]
                           name                                     
description
12  with_illumina_humanwg_6_v1               with Illumina HumanWG 6 v1 
ID(s))
13  with_illumina_humanwg_6_v2                with Illumina HumanWG 6 v2 
ID(s)
14  with_illumina_humanwg_6_v3                with Illumina HumanWG 6 v3 
ID(s)
15    with_illumina_humanht_12                 with Illumina Human HT 12 
ID(s)
125      illumina_humanwg_6_v1   Illumina HumanWG 6 V1 ID(s) [e.g. 
0000940471]
126      illumina_humanwg_6_v2 Illumina HumanWG 6 V2 ID(s) [e.g. 
ILMN_1748182]
127      illumina_humanwg_6_v3 Illumina HumanWG 6 v3 ID(s) [e.g. 
ILMN_2103362]
128        illumina_humanht_12  Illumina Human HT 12 ID(s) [e.g. 
ILMN_1672925]

Many Thanks,
Natasha


On 18/08/2011 15:04, Hervé Pagès wrote:
> Natasha,
>
> On 11-08-18 06:32 AM, Natasha Sahgal wrote:
>> Dear All,
>>
>> Please ignore this, as now it does appear to work. I do wonder, why did
>> it not work earlier though.
>>
>> Also, could someone please tell me the difference between
>> "with_illumina_humanht_12" and "illumina_humanht_12" in the filters and
>> attributes?
>
> I don't see the "with_illumina_humanht_12" attribute:
>
>   library(biomaRt)
>   ensembl =  useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", 
> dataset="hsapiens_gene_ensembl")
>   atts = listAttributes(ensembl)
>
> Then:
>
> > atts[grep("illumina", atts[[1]], ignore.case=TRUE), ]
>                        name           description
>   104 illumina_humanwg_6_v1 Illumina HumanWG 6 v1
>   105 illumina_humanwg_6_v2 Illumina HumanWG 6 v2
>   106 illumina_humanwg_6_v3 Illumina HumanWG 6 v3
>   107   illumina_humanht_12  Illumina Human HT 12
>
>> What version of the illumina_humanht_12 chip is used, as this is 
>> unclear?
>
> According to the Illumina website the latest version of this chip seems
> to be v4 but it's not clear indeed that the Emsembl folks are referring
> to that one. You might want to ask them directly (biomaRt is just a tool
> to query data their data).
>
> Cheers,
> H.
>
>>
>>
>> Many Thanks,
>> Natasha
>>
>> On 18/08/2011 11:02, Natasha Sahgal wrote:
>>> Dear List,
>>>
>>> I am using biomaRt for the first time.
>>>
>>> Initially I had problems connecting to hsapiens dataset, though I
>>> could listMarts. However that issue was resolved (by solutions in some
>>> earlier posts) by changing the host to www.ensembl.org.
>>>
>>> Now though I get the following error message when I try to execute the
>>> following command:
>>>
>>> >mg_eg.ens.t <- getBM(attributes =
>>> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbol"), 
>>>
>>> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = 
>>> ensembl)
>>>
>>>
>>> V1
>>> 1 <head>
>>> 2 <link rel=Shortcut Icon href=/errors/ensembl_ico.png 
>>> type=image/png />
>>> 3 <title>The Ensembl Genome Browser</title>
>>> 4 <style type=text/css>
>>> 5
>>> body{color:#333333;background-color:#eaeeff;font-family:Arial,Helvetica,Sans-serif;font-size:14pt;margin:0;padding:0} 
>>>
>>>
>>> 6
>>> #masthead{color:#ffffff;background-color:#333366;width:100%;height:50px;padding:5px 
>>>
>>> 0;font-size:1.75em;text-align:center;margin:auto}
>>> Error in getBM(attributes = c("entrezgene", "ensembl_gene_id",
>>> "ensembl_transcript_id", :
>>> The query to the BioMart webservice returned an invalid result: the
>>> number of columns in the result table does not equal the number of
>>> attributes in the query. Please report this to the mailing list.
>>>
>>>
>>> This I found strange as I did the same thing yesterday with another
>>> object and it worked!!
>>>
>>> Full Code and SessionInfo:
>>>
>>> head(mg.u.eg$Entrez_Gene_ID) #[1] 27122 3488 72 1293 100134134 390
>>>
>>> length(mg.u.eg$Entrez_Gene_ID) #[1] 4288
>>>
>>>
>>> listMarts(host="www.ensembl.org")
>>> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
>>> listDatasets(ensembl)
>>> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org",
>>> dataset="hsapiens_gene_ensembl")
>>> filt = listFilters(ensembl)
>>> atts = listAttributes(ensembl)
>>>
>>> mg_eg.ens <- getBM(attributes =
>>> c("entrezgene","ensembl_gene_id","hgnc_symbol"), filters =
>>> "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) # 4016 3
>>>
>>> mg_eg.ens.t <- getBM(attributes =
>>> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbol"), 
>>>
>>> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = 
>>> ensembl)
>>>
>>> sessionInfo()
>>> R version 2.13.0 (2011-04-13)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
>>> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8
>>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] biomaRt_2.8.0 DESeq_1.4.1 locfit_1.5-6 lattice_0.19-23
>>> [5] akima_0.5-4 Biobase_2.12.1 WriteXLS_2.1.0 gdata_2.8.2
>>> [9] limma_3.8.2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5
>>> [4] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0
>>> [7] gtools_2.6.2 RColorBrewer_1.0-2 RCurl_1.6-4
>>> [10] RSQLite_0.9-4 splines_2.13.0 survival_2.36-5
>>> [13] tools_2.13.0 XML_3.4-0 xtable_1.5-6
>>>
>>>
>>> Many Thanks,
>>> Natasha
>>>
>>> -- 
>>>
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>>
>> _______________________________________________
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>
>

-- 

Natasha Sahgal, PhD

Research Associate in Functional Genomics
Bioinformatics&  Statistical Genetics Core
Wellcome Trust Center for Human Genetics
University of Oxford
Roosevelt Drive
Oxford OX3 7BN
U.K.

Tel: + 44 -(0)1865 287 609
Fax: + 44 -(0)1865 287 664

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