[BioC] biomaRt query

[Steffen at stat.Berkeley.EDU]

Hi Tim,

Do you specifically need Ensembl version 49 or would another Ensembl
version using NCBI36 do?

The error is probably generated because 49 is old and some changes to the
BioMart API occured after version 50 I think.  You can access Ensembl 54
which is also using NCBI36, by doing the following:

ensembl=useMart(host="may2009.archive.ensembl.org",biomart="ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl")

locations <- getBM(c('entrezgene','hgnc_symbol','chromosome_name',
+                  'start_position','end_position'), filters="entrezgene",
+        values=entrezIDs, mart=ensembl)

> locations
  entrezgene hgnc_symbol chromosome_name start_position end_position
1      10857      PGRMC1               X      118254279    118262456
2       5055    SERPINB2              18       59689906     59722100
3       8334   HIST1H2AC               6       26232352     26292434
4       8349   HIST2H2BE               1      148080395    148124826
5      85236   HIST1H2BK               6       27214052     27222598


Note that you can find the correct host names to use for specific Ensembl
versions by going to http://www.ensembl.org and then at the bottom of the
page, click on "view in archive site", select an archive and then copy the
url.

Hope this helps,
Steffen

> Hi,
>
> I wanted to query on the NCBI36 build, and built the following query:
> ----------------------------------------
> entrezIDs <- c("8334","85236","10857","8349","5055") # sample list of ids
>   ensembl <- useMart(biomart="ensembl",
> dataset="hsapiens_gene_ensembl",archive=TRUE) #"ensembl_mart_49"
>   locations <- getBM(c('entrezgene','hgnc_symbol','chromosome_name',
>                  'start_position','end_position'), filters="entrezgene",
>        values=entrezIDs, mart=ensembl)
> _________________________________
>
>
> I get the following error:
> Error in listFilters(mart, what = "type") :
>   The function argument 'what' contains an invalid value: type
> Valid are: name, description, options, fullDescription, filters5, filters6
>
>
> How should I modify the query? If I use the query with the current/default
> version of ensembl, the query executes ok.
> thanks!
> My sessionInfo() is:
> -----------------
> R version 2.9.1 (2009-06-26)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] grid      stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
>  [1] e1071_1.5-19        class_7.2-47        org.Hs.eg.db_2.2.11
>  [4] GOstats_2.10.0      graph_1.22.2        Category_2.10.1
>  [7] GO.db_2.2.11        biomaRt_2.0.0       multtest_2.1.1
> [10] XML_2.5-3           genefilter_1.24.2   hgu133a.db_2.2.12
> [13] RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.6.1
> [16] GEOquery_2.8.0      RCurl_0.98-1        affy_1.22.0
> [19] Biobase_2.4.1       gplots_2.7.1        caTools_1.9
> [22] bitops_1.0-4.1      gdata_2.6.1         gtools_2.6.1
> [25] lattice_0.17-25
>
> loaded via a namespace (and not attached):
>  [1] affyio_1.12.0        annotate_1.22.0      GSEABase_1.6.1
>  [4] MASS_7.2-47          preprocessCore_1.6.0 RBGL_1.20.0
>  [7] splines_2.9.1        survival_2.35-4      tools_2.9.1
> [10] xtable_1.5-5
>>
>
>
>
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>
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