Hi, I am using biomaRt to retrieve gene annotation using Ensembl IDs, and the exact same code that worked properly just a month ago, now throws errors.

Please check the MWE below:

library(biomaRt)
ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl", host="www.ensembl.org")

genes <- c("ENSG00000121671", "ENSG00000142208", "ENSG00000171051", "ENSG00000115271", "ENSG00000143537")

getBM(attributes=c('ensembl_gene_id','entrezgene','hgnc_id','hgnc_symbol'), filters='ensembl_gene_id', values=genes, mart=ensembl)

And the error it returns:

Error in getBM(attributes = c("ensembl_gene_id", "entrezgene", "hgnc_id",  : 
  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.

Has anything changed over the last month and things have to be done differently now? Is there anything wrong with my code? Thanks!

It seems it is working for some people, so I include my sessionInfo() output below, to see if someone can spot what the problem is. Thanks!

 

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.5

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_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] biomaRt_2.32.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11         IRanges_2.10.2       XML_3.98-1.7         digest_0.6.12        bitops_1.0-6        
 [6] DBI_0.6-1            stats4_3.4.0         RSQLite_1.1-2        S4Vectors_0.14.3     tools_3.4.0         
[11] Biobase_2.36.2       RCurl_1.95-4.8       parallel_3.4.0       compiler_3.4.0       BiocGenerics_0.22.0 
[16] AnnotationDbi_1.38.1 memoise_1.1.0       

I got different error message when I was running BiomaRt:::getBM.

You could look at ensembldb or EnsDb.Hsapiens if you are trying to convert IDs.

Elaborating a little on Haiying's suggestion: first load one of the EnsDbs from AnnotationHub. They have an updated database scheme that provides a better mapping between Ensembl gene IDs and Entrezgene IDs (for Ensembl gene IDs mapping to multiple Entrezgene IDs you'll get all of them individually, not comma separated as a single string)

library(AnnotationHub)
## Fetch the EnsDb for Ensembl version 87
edb <- query(AnnotationHub(), "EnsDb.Hsapiens.v87")[[1]]

genes <- c("ENSG00000121671", "ENSG00000142208", "ENSG00000171051", "ENSG00000115271", "ENSG00000143537")

## Use the select method to fetch the data
res <- select(edb, columns = c("ENTREZID", "GENENAME"), keys = genes, keytype = "GENEID")
res
           GENEID ENTREZID GENENAME
1 ENSG00000121671     1408     CRY2
2 ENSG00000142208      207     AKT1
3 ENSG00000171051     2357     FPR1
4 ENSG00000115271    25801      GCA
5 ENSG00000143537     8751   ADAM15

hope this helps.

cheers, jo

I suspect this problem was related to the update to Ensembl 89 (i.e. Ensembl 89 has been released) and you were unfortunate to query during the transition time.  For me the code seems to work fine now e.g.

getBM(attributes= c('ensembl_gene_id','entrezgene','hgnc_id','hgnc_symbol'), 
      filters = 'ensembl_gene_id', 
      values = genes, 
      mart = ensembl)

  ensembl_gene_id entrezgene    hgnc_id hgnc_symbol
1 ENSG00000115271      25801 HGNC:15990         GCA
2 ENSG00000121671       1408  HGNC:2385        CRY2
3 ENSG00000142208        207   HGNC:391        AKT1
4 ENSG00000143537       8751   HGNC:193      ADAM15
5 ENSG00000171051       2357  HGNC:3826        FPR1

In case you're running an old version of biomaRt, here's my session information

> sessionInfo()

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 18.1

Matrix products: default
BLAS: /home/msmith/Applications/R/R-3.4.0/lib/libRblas.so
LAPACK: /home/msmith/Applications/R/R-3.4.0/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] biomaRt_2.33.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11         IRanges_2.11.3       XML_3.98-1.7         prettyunits_1.0.2    assertthat_0.2.0    
 [6] digest_0.6.12        bitops_1.0-6         R6_2.2.1             DBI_0.6-1            magrittr_1.5        
[11] stats4_3.4.0         RSQLite_1.1-2        progress_1.1.2       S4Vectors_0.15.2     tools_3.4.0         
[16] Biobase_2.37.2       RCurl_1.95-4.8       parallel_3.4.0       compiler_3.4.0       BiocGenerics_0.23.0 
[21] AnnotationDbi_1.39.0 memoise_1.1.0