Dear James and Steffen,

 thanks , workks properly now. At the same time seems that the functions
defined in biomaRt do not work on
the archived versions.

#######
> ensmart       <-
useMart("ensembl_mart_37",dataset="hsapiens_gene_ensembl",mysql=TRUE,archive=TRUE)
connected to:  ensembl_mart_37
Reading database configuration of: hsapiens_gene_ensembl
Checking attributes and filters ... ok
Checking main tables ... ok
>  gene.list           <- getFeature(chromosome=1,type="entrezgene",
mart=ensmart)
Error in getFeature(chromosome = 1, type = "entrezgene", mart = ensmart) :
    This function only works when using to ensembl. To use this function
use: mart =  useMart('ensembl')
########

R version 2.5.0 (2007-04-23)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "datasets"
[7] "utils"     "methods"   "base"

other attached packages:
        RSNPper        multtest         GOstats        Category
Matrix
       "1.10.0"        "1.14.0"         "2.2.6"         "2.2.3"     "
0.99875-2"
        lattice      genefilter        survival            KEGG
RBGL
       "0.15-4"        "1.14.1"          "2.31"        "1.16.1"        "
1.12.0"
       annotate         Biobase              GO           graph
matlab
       "1.14.1"        "1.14.0"        "1.16.0"        "1.14.2"         "
0.8-1"
humanLLMappings          RMySQL             DBI         biomaRt
RCurl
       "1.16.0"         "0.6-0"         "0.2-3"        "1.10.0"         "
0.8-0"
            XML
        "1.9-0"


On 6/27/07, James W. MacDonald <jmacdon@med.umich.edu> wrote:
>
> I think you simply need the _current_ version of BioC packages:
>
> > mart <-
>
> useMart("ensembl_mart_44",dataset="hsapiens_gene_ensembl",mysql=TRUE,archive=TRUE)
> connected to:  ensembl_mart_44
> Reading database configuration of: hsapiens_gene_ensembl
> Checking attributes and filters ... ok
> Checking main tables ... ok
> > sessionInfo()
> R version 2.5.0 (2007-04-23)
> 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] "stats"     "graphics"  "grDevices"
> [4] "datasets"  "utils"     "methods"
> [7] "base"
>
> other attached packages:
>    RMySQL      DBI  biomaRt    RCurl      XML
> "0.5-11"  "0.2-3" "1.10.0"  "0.8-0"  "1.7-1"
>
> Best,
>
> Jim
>
>
> > marco zucchelli wrote:
> > Dear Steffen,
> >
> >  seems like it does not work ("archive" is not accepted). Maybe  I need
> the
> > developer version of biomaRt ?
> >
> >
> > ######
> >> ensembl =
> >
> useMart("ensembl_mart_44",dataset="hsapiens_gene_ensembl",mysql=TRUE,archive=TRUE)
> > Error in useMart("ensembl_mart_44", dataset =
> "hsapiens_gene_ensembl",  :
> >     unused argument(s) (archive = TRUE)
> >> sessionInfo()
> > R version 2.4.1 (2006-12-18)
> > x86_64-unknown-linux-gnu
> >
> > locale:
> >
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> > attached base packages:
> > [1] "splines"   "tools"     "stats"     "graphics"  "grDevices"
> "datasets"
> > [7] "utils"     "methods"   "base"
> >
> > other attached packages:
> >      RMySQL         DBI     biomaRt       RCurl         XML     annaffy
> >     "0.6-0"     "0.2-3"     "1.8.2"     "0.8-0"     "1.6-3"     "1.6.2"
> >         vsn     affyPLM       gcrma matchprobes    affydata    multtest
> >    "1.12.0"    "1.10.0"     "2.6.0"     "1.6.0"    "1.10.0"    "1.12.0"
> >     GOstats    Category  genefilter    survival        KEGG        RBGL
> >     "2.0.4"     "2.0.3"    "1.12.0"      "2.30"    "1.14.1"    "1.10.0"
> >       graph     goTools    annotate          GO      matlab       limma
> >    "1.12.1"     "1.6.0"    "1.12.1"    "1.14.1"     "0.8-1"    "2.9.17"
> > hgu133plus2        affy      affyio     Biobase
> >    "1.14.0"    "1.12.2"     "1.2.0"    "1.12.2"
> >
> >> listMarts(mysql=TRUE)
> > [1] "ensembl_mart_45"  "vega_mart_45"     "snp_mart_45"
> > "sequence_mart_45"
> > [5] "danio_snp_mart"   "msd_mart_4"       "uniprot_mart_17"
> > ############
> >
> >
> > Cheers
> >
> > Marco
> >
> >
> > On 6/20/07, Durinck, Steffen (NIH/NCI) [F] <durincks@mail.nih.gov>
> wrote:
> >> Dear Marco,
> >>
> >> Selecting archived versions is currently only possible using biomaRt in
> >> MySQL mode and will become available soon in web service mode.
> >>
> >> To see the available archives do:
> >>
> >> listMarts(mysql=TRUE, archive=TRUE)
> >>
> >> To connect to a previous version (e.g. Ensembl 44) you have to do:
> >>
> >> ensembl =
> >>
> useMart("ensembl_mart_44",dataset="hsapiens_gene_ensembl",mysql=TRUE,archive=TRUE)
> >>
> >> Use the listDatasets function to see the NCBI version, you'll have to
> go
> >> back to Ensembl 37 to get the NCBI35 build.
> >>
> >> Cheers,
> >> Steffen
> >>
> >> -----Original Message-----
> >> From: marco zucchelli [mailto:marco.bioc@gmail.com]
> >> Sent: Tue 6/19/2007 7:12 AM
> >> To: bioconductor
> >> Subject: [BioC] Biomart with human genes NCBI 35
> >>
> >> Dear All,
> >>
> >> is it possible to select within biomart other builds for human genes
> >> rather
> >> than the current
> >> NCBI36 ?
> >> I would like to get  gene positions according to  NCBI35  but seems
> that
> >> there is no way to
> >> do that
> >>
> >> Regards
> >>
> >> Marco
> >>
> >>         [[alternative HTML version deleted]]
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor@stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >>
> >>
> >
> >       [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should not
> be used for urgent or sensitive issues.
>

	[[alternative HTML version deleted]]

