[BioC] Biomart with human genes NCBI 35

[James W. MacDonald]

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 at 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 at 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]]
>>
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>>
> 
> 	[[alternative HTML version deleted]]
> 
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