[BioC] biomart error

Thu Aug 18 16:04:06 CEST 2011

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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-- 
Hervé Pagès

Program in Computational Biology
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