Question: The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query
2
gravatar for ang
18 months ago by
ang20
ang20 wrote:

Hi

Reporting this biomaRt error which has been occurring recurrently over the last week

biomaRt error :: The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.

All attributes appear valid. I have also tried subsetting on a smaller number of attributes without success.

Advice, input and resolution welcome.

Cheers. Ashley

> library(biomaRt)
> listMarts(host="www.ensembl.org")
> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host="www.ensembl.org")
> listAttributes(human)
> attributes = c("ensembl_gene_id", "hgnc_symbol", "mmusculus_homolog_ensembl_gene", "mmusculus_homolog_associated_gene_name", "mmusculus_homolog_perc_id_r1")
> listFilters(human, what = c("name", "description"))
> orth.mouse = getBM(attributes,filters="with_mmusculus_homolog",values=TRUE, mart = human,uniqueRows=TRUE)


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1                                                                                                                                     <html><head>
2                                                                                                                         <title>302 Found</title>
3                                                                                                                                    </head><body>
4                                                                                                                                   <h1>Found</h1>
5 <p>The document has moved <a href=//asia.ensembl.org/biomart/martservice?;redirectsrc=//www.ensembl.org%2Fbiomart%2Fmartservice%3F>here</a>.</p>
6                                                                                                                                   </body></html>
Error in getBM(attributes, filters = "with_mmusculus_homolog", values = TRUE,  : 
  The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list.
> sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.32.1       BiocInstaller_1.26.1 edgeR_3.18.1         AnnotationDbi_1.38.2 IRanges_2.10.5      
[6] S4Vectors_0.14.7     Biobase_2.36.2       BiocGenerics_0.22.1  limma_3.32.10       

ADD COMMENTlink modified 18 months ago by thokall160 • written 18 months ago by ang20
1

I have made some more updates to biomaRt, available in version 2.35.4 ( BiocInstaller::biocLite('grimbough/biomaRt') ), hopefully this fixes things.  

Since this seems to be affecting a lot of people, it would be really helpful if anyone experiencing the problem could provide a small example, along with their location the world.  You can do this at this Github issue (https://github.com/grimbough/biomaRt/issues/1)

I'm also in discussion with the Ensembl team to determine the best way forward in the future.

 

ADD REPLYlink modified 18 months ago • written 18 months ago by Mike Smith3.7k
Answer: The query to the BioMart webservice returned an invalid result: the number of co
3
gravatar for thokall
18 months ago by
thokall160
Swedish Museum of Natural History
thokall160 wrote:

There appear to some issues with the release of ensembl ver. 91 some days ago perhaps your problem is related to this. See for example: C: biomaRt: drerio_gene_ensembl dataset missing

So try to to either install a patched version via GitHub

BiocInstaller::biocLite('grimbough/biomaRt')

and load the library again. Or consider using an older version of the ensembl data. The following will use version 90.

human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", "http://Aug2017.archive.ensembl.org")
ADD COMMENTlink written 18 months ago by thokall160
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