Biomart getLDS error
4
0
Entering edit mode
Diwan • 0
@diwan-7291
Last seen 6.0 years ago
United States

Hello,

I am trying to use biomaRt to convert human ensembl gene ids to rat gene ids. I have previously used this and it worked perfectly. But, now I am getting an error message. My problem with an exemplar is given below.

library("biomaRt")

human <- useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
rat   <- useMart(host="www.ensembl.org", "ENSEMBL_MART_ENSEMBL", dataset="rnorvegicus_gene_ensembl")

getLDS(attributes=c("ensembl_gene_id","hgnc_symbol"), filters="ensembl_gene_id", values= "ENSG00000165029", mart=human, attributesL=c("entrezgene","rgd_symbol"), martL=rat)

I get the error message:

Error in getLDS(attributes = c("ensembl_gene_id", "hgnc_symbol"), filters = "ensembl_gene_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.

Only "getLDS" function produces error. For example, when I try "getBM" it works fine. 

getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id", "entrezgene", "hgnc_symbol"),values= "ENSG00000165029",mart= human)

OUTPUT:

ensembl_gene_id entrezgene hgnc_symbol
1 ENSG00000165029         19       ABCA1

Any help is greatly appreciated.

Thanks

Diwan

sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] RCurl_1.95-4.7                       bitops_1.0-6                        
 [3] BiocInstaller_1.18.5                 biomaRt_2.24.0                      
 [5] annotate_1.46.1                      XML_3.98-1.3                        
 [7] pd.ragene.2.1.st_3.14.1              oligo_1.32.0                        
 [9] oligoClasses_1.30.0                  Biostrings_2.36.4                   
[11] XVector_0.8.0                        ragene21sttranscriptcluster.db_8.3.1
[13] ragene21stprobeset.db_8.3.1          org.Rn.eg.db_3.1.2                  
[15] RSQLite_1.0.0                        DBI_0.3.1                           
[17] AnnotationDbi_1.30.1                 GenomeInfoDb_1.4.2                  
[19] IRanges_2.2.7                        S4Vectors_0.6.4                     
[21] Biobase_2.28.0                       BiocGenerics_0.14.0                 

loaded via a namespace (and not attached):
 [1] affxparser_1.40.0     splines_3.2.2         GenomicRanges_1.20.6  zlibbioc_1.14.0      
 [5] bit_1.1-12            xtable_1.7-4          foreach_1.4.2         tools_3.2.2          
 [9] ff_2.2-13             iterators_1.0.7       preprocessCore_1.30.0 affyio_1.36.0        
[13] codetools_0.2-14

 

 

biomart getLDS orthlog • 2.3k views
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2
Entering edit mode
Mike Smith ★ 5.8k
@mike-smith
Last seen 6 hours ago
EMBL Heidelberg / de.NBI

I think this is related to the error reported in Error in biomaRt User Guide example Task 11

It looks like the ortholog functionality in Ensembl Biomart is currently not functioning how it did previously, and you cannot get this information using either the biomaRt package or the web interface.  A temporary solution is to use the most recent archive like so:

library('biomaRt')

human.old <- useMart(host="jul2016.archive.ensembl.org", 
                     "ENSEMBL_MART_ENSEMBL", 
                     dataset="hsapiens_gene_ensembl")

rat.old   <- useMart(host="jul2016.archive.ensembl.org", 
                     "ENSEMBL_MART_ENSEMBL", 
                     dataset="rnorvegicus_gene_ensembl")

getLDS(attributes = c("ensembl_gene_id","hgnc_symbol"), 
       filters = "ensembl_gene_id", 
       values = "ENSG00000165029", 
       mart = human.old, 
       attributesL = c("entrezgene","rgd_symbol"),
       martL = rat.old)
  Ensembl.Gene.ID HGNC.symbol EntrezGene.ID RGD.Symbol
1 ENSG00000165029       ABCA1        313210      Abca1

The release notes for Ensembl 86 say the have made changes to the ortholog tables, so it may be worth enquiring with them whether there is another way to access this information.

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2
Entering edit mode
Thomas Maurel ▴ 790
@thomas-maurel-5295
Last seen 9 months ago
United Kingdom

I am afraid that we have a bug affecting the multiple datasets selection in the release 86 gene mart. This is causing the BiomaRt getLDS function to fail over.

We have a working fix that we will push live early next week, I will let you know as soon as the release 86 gene mart is working again.

In the meantime, please feel free to use our previous release e!85 marts:

human <- useMart("ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "e85.ensembl.org")

Apologies for any inconvenience caused,
Best Regards,
Thomas

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1
Entering edit mode
Thomas Maurel ▴ 790
@thomas-maurel-5295
Last seen 9 months ago
United Kingdom

Just to let you know that we have now pushed a fix to our main website www.ensembl.org, you can access it by running:

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

We will fix the US West, US East and Asian mirrors next week.

Thank you for your patience.
Best Regards,
Thomas

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0
Entering edit mode

Thanks very much for pushing the patch Thomas, it looks like it's working fine for me now.

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0
Entering edit mode
Thomas Maurel ▴ 790
@thomas-maurel-5295
Last seen 9 months ago
United Kingdom

Just to let you know that the US West, US East and Asian mirrors have now been fixed too.

Thank you for your patience.
Best Regards,
Thomas

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0
Entering edit mode

I am using the database today. It worked fine for the past 3 month but suddenly today I got the same error as above when I used useast.ensembl.org

I used e85 and it ran fine

Is it the same bug?

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0
Entering edit mode

I am afraid this is a different problem, Mike has fixed it and the fix should be propagated in the coming days: A: biomaRt: drerio_gene_ensembl dataset missing

Kind Regards,

Thomas

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