[BioC] biomaRt, Error: ncol(result) == length(attributes) is not TRUE

[Dick Beyer]

Hi Steffen,

Thanks for your quick response.  I did the upgrade to 1.9.29 and everything works!

Thanks very much,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
*******************************************************************************

On Fri, 20 Apr 2007, Steffen Durinck wrote:

> Hi Dick,
>
> Not sure what's going wrong, try updating to the 1.9.29 devel version of the 
> package.
> I tried your query and have no problems:
>
> getGO(id=3064,type="entrezgene",mart=mart)
>  entrezgene         go                       go_description evidence_code
> 1        3064 GO:0003714   transcription corepressor activity           TAS
> 2        3064 GO:0005215                 transporter activity           TAS
> 3        3064 GO:0005515                      protein binding           IPI
> 4        3064 GO:0005625                     soluble fraction           TAS
> 5        3064 GO:0005634                              nucleus           TAS
> ....
>
> Best regards,
> Steffen
>
> Dick Beyer wrote:
>> I'm having difficulty getting biomaRt getGO() to work.  Here is a typical 
>> session:
>> 
>>   
>>> library(biomaRt)
>>>     
>> 
>>   
>>> mart <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
>>>     
>> Checking attributes and filters ... ok
>> 
>>   
>>> g <- getGO(id=3064,type="entrezgene",mart=mart)
>>>     
>> Error: ncol(result) == length(attributes) is not TRUE
>> 
>> 
>>   
>>> listDatasets(mart)
>>>     
>>                            dataset    version
>> 1          oanatinus_gene_ensembl      OANA5
>> 2         gaculeatus_gene_ensembl    BROADS1
>> 3         cporcellus_gene_ensembl  GUINEAPIG
>> 4          lafricana_gene_ensembl    BROADE1
>> 5  stridecemlineatus_gene_ensembl   SQUIRREL
>> 6        scerevisiae_gene_ensembl    SGD1.01
>> 7         eeuropaeus_gene_ensembl   HEDGEHOG
>> 8          etelfairi_gene_ensembl     TENREC
>> 9       ptroglodytes_gene_ensembl   CHIMP2.1
>> 10     cintestinalis_gene_ensembl       JGI2
>> 11        ocuniculus_gene_ensembl     RABBIT
>> 12          hsapiens_gene_ensembl     NCBI36
>> 13           ggallus_gene_ensembl    WASHUC2
>> 14        tbelangeri_gene_ensembl  TREESHREW
>> 15     tnigroviridis_gene_ensembl TETRAODON7
>> 16          mmulatta_gene_ensembl     MMUL_1
>> 17          mmusculus_miscfeature    NCBIM36
>> 18          olatipes_gene_ensembl    MEDAKA1
>> 19           hsapiens_miscfeature     NCBI36
>> 20           btaurus_gene_ensembl   Btau_3.1
>> 21          aaegypti_gene_ensembl     AaegL1
>> 22         csavignyi_gene_ensembl    CSAV2.0
>> 23       rnorvegicus_gene_ensembl    RGSC3.4
>> 24            fcatus_gene_ensembl        CAT
>> 25          celegans_gene_ensembl      WB170
>> 26         trubripes_gene_ensembl      FUGU4
>> 27           agambiae_miscfeature     AgamP3
>> 28     dnovemcinctus_gene_ensembl       ARMA
>> 29          agambiae_gene_ensembl     AgamP3
>> 30        mlucifugus_gene_ensembl  MICROBAT1
>> 31       xtropicalis_gene_ensembl     JGI4.1
>> 32            drerio_gene_ensembl     ZFISH6
>> 33        mdomestica_gene_ensembl    BROADO3
>> 34        ogarnettii_gene_ensembl  BUSHBABY1
>> 35     dmelanogaster_gene_ensembl    BDGP4.3
>> 36         mmusculus_gene_ensembl    NCBIM36
>> 37       cfamiliaris_gene_ensembl    BROADD2
>> 
>> sessionInfo()
>> R version 2.4.1 (2006-12-18) 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] "tools"     "stats"     "graphics"  "grDevices" "utils"     "datasets" 
>> "methods"   "base"
>> 
>> other attached packages:
>>      biomaRt       RCurl         XML   Rgraphviz geneplotter       graph 
>> annotate     Biobase          GO
>>      "1.8.2"     "0.8-0"     "1.1-1"    "1.12.1"    "1.12.0"    "1.12.0" 
>> "1.12.0"    "1.12.2"    "1.14.0"
>> 
>> I tried many variations of arguments to getGO and getGene.  I tried the 
>> examples in the help, but still got the same error.
>> 
>> If anyone had some suggestions, I would be most grateful.
>> 
>> Thanks much,
>> Dick
>> *******************************************************************************
>> Richard P. Beyer, Ph.D.	University of Washington
>> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
>> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
>>  			Seattle, WA 98105-6099
>> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
>> http://staff.washington.edu/~dbeyer
>> 
>> _______________________________________________
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>>   
>
>
> -- 
> Steffen Durinck, Ph.D.
>
> Oncogenomics Section
> Pediatric Oncology Branch
> National Cancer Institute, National Institutes of Health
> URL: http://home.ccr.cancer.gov/oncology/oncogenomics/
>
> Phone: 301-402-8103
> Address:
> Advanced Technology Center,
> 8717 Grovemont Circle
> Gaithersburg, MD 20877
>