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

[Steffen Durinck]

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