[BioC] Error using makeGeneRegion/getBM/listFilters, argument 'what' contains an invalid value: type

[Steffen at stat.Berkeley.EDU]

Hi Tejal,

You'll need to do your query using the web interface at:

http://aug2007.archive.ensembl.org/biomart/martview/

export as a tab delimited file and import that in R.

Cheers,
Steffen

> Hi Steffen,
> You are right, this version is too old, but I need to use the older
> version.
> Any suggestions ?
>
> -Tejal
>
> On Wed, Nov 11, 2009 at 5:49 PM, <Steffen at stat.berkeley.edu> wrote:
>
>> Hi Tejal,
>>
>> Ensembl 46 is to old and there have been some major changes since for
>> biomaRt to work with it.  Would a more recent ensembl archive work for
>> you?
>> For example Ensembl 54 is NCBI36 and might be what you were looking for
>> unless you have another reason to specifically want Ensembl 46?
>> You can access Ensembl 54 like this:
>>
>> > listMarts(host="may2009.archive.ensembl.org/biomart/martservice")
>>               biomart              version
>> 1 ENSEMBL_MART_ENSEMBL           Ensembl 54
>> 2     ENSEMBL_MART_SNP Ensembl Variation 54
>> 3    ENSEMBL_MART_VEGA              Vega 35
>> 4             REACTOME   Reactome(CSHL US)
>> 5     wormbase_current   WormBase (CSHL US)
>> 6                pride       PRIDE (EBI UK)
>> > ens54 = useMart("ENSEMBL_MART_ENSEMBL",
>> dataset="hsapiens_gene_ensembl"
>> ,host="may2009.archive.ensembl.org/biomart/martservice")
>> Checking attributes and filters ... ok
>>
>>
>>
>> Cheers,
>> Steffen
>>
>>
>>
>> > Hi,
>> > I have been trying to work with an archived version of ensembl mart,
>> i.e.
>> > ensembl_46. The code goes as follow:
>> >
>> >>library(biomaRt)
>> >>#listMarts(archive=TRUE)
>> >>mart=useMart("ensembl_mart_46", archive=TRUE)
>> >>## listDatasets(mart)
>> >>mart=useDataset("mmusculus_gene_ensembl",mart)
>> > Checking attributes ... ok
>> > Checking filters ... ok
>> > Warning messages:
>> > 1: In bmAttrFilt("attributes", mart) :
>> >   biomaRt warning: looks like we're connecting to an older version of
>> > BioMart suite. Some biomaRt functions might not work.
>> > 2: In bmAttrFilt("filters", mart) :
>> >   biomaRt warning: looks like we're connecting to an older version of
>> > BioMart suite. Some biomaRt functions might not work.
>> >
>> >> plusStrand = new("GeneRegion", chromosome = "17", start = 30450000,
>> end
>> >> =
>> > 30550000, strand = "+", biomart = mart)
>> >
>> >
>> > I have modified the GeneRegion method such that it can work with
>> older,
>> > hardcoded attribute names. It started to give error once again due to
>> > "strand" not being one of the filters supported by old ensembl build.
>> > Therefore, I tried a simpler way to collect genomic features from
>> biomart
>> > :
>> >
>> >  > getBM(c("gene_stable_id","transcript_stable_id",
>> >
>> > "exon_stable_id","exon_chrom_start","exon_chrom_end",
>> >                                 "rank",
>> > "transcript_chrom_strand","struct_biotype"),
>> >
>> >
>> filters=c("chromosome_name","start","end"),values=list(17,30450000,30455000),mart)
>> >
>> > Error in listFilters(mart, what = "type") :
>> > The function argument 'what' contains an invalid value: type
>> > Valid are: name, description, options, fullDescription
>> >
>> > I also tried out with listFilters function :
>> > listFilters("chromosome_name",mart=mart), which results in the same
>> error.
>> >
>> > What is going on here, and how can I rectify it ?
>> >
>> > Here is my session info:
>> >
>> > R version 2.9.1 (2009-06-26)
>> > 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] grid      stats     graphics  grDevices utils     datasets
>> methods
>> > base
>> >
>> > other attached packages:
>> > [1] GenomeGraphs_1.0.1 biomaRt_2.0.0
>> >
>> > loaded via a namespace (and not attached):
>> > [1] RCurl_0.94-1 XML_2.6-0
>> >
>> >
>> > Thanks,
>> > Tejal
>> >
>> >       [[alternative HTML version deleted]]
>> >
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>> >
>>
>>
>