biomaRt error in getBM for hsapiens_gene_ensembl
4
1
Entering edit mode
rbacher ▴ 20
@rbacher-12895
Last seen 19 months ago

I'm getting the following error when I try to use the getBM() function with any attributes:

> library(biomaRt)
> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> getBM(c("hgnc_symbol"), "hgnc_symbol", "MLK2", mart= human)​

 

                                                                                                    <!DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN>
1                                                                                                                                       <html><head>
2                                                                                                                           <title>302 Found</title>
3                                                                                                                                      </head><body>
4                                                                                                                                     <h1>Found</h1>
5 <p>The document has moved <a href=//useast.ensembl.org/biomart/martservice?;redirectsrc=//www.ensembl.org%2Fbiomart%2Fmartservice%3F>here</a>.</p>
6                                                                                                                                     </body></html>
Warning message:
In .setResultColNames(result, mart = mart, attributes = attributes,  :
 Problems assigning column names.Currently using the biomart description field.You may wish to set these manually.​

Any help is appreciated!

Thanks,

Rhonda

 

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.1

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_2.35.1       BiocInstaller_1.28.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14         AnnotationDbi_1.40.0 knitr_1.17           magrittr_1.5         devtools_1.13.4      BiocGenerics_0.24.0 
 [7] progress_1.1.2       IRanges_2.12.0       bit_1.1-12           R6_2.2.2             rlang_0.1.2          httr_1.3.1          
[13] stringr_1.2.0        blob_1.1.0           tools_3.4.1          parallel_3.4.1       Biobase_2.38.0       DBI_0.7             
[19] git2r_0.19.0         withr_2.0.0          yaml_2.1.14          bit64_0.9-7          digest_0.6.12        assertthat_0.2.0    
[25] tibble_1.3.4         S4Vectors_0.16.0     bitops_1.0-6         curl_3.0             RCurl_1.95-4.8       memoise_1.1.0       
[31] RSQLite_2.0          stringi_1.1.5        compiler_3.4.1       prettyunits_1.0.2    stats4_3.4.1         XML_3.98-1.9       

 

 

 

 

 

 

 

 
biomart • 2.0k views
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1
Entering edit mode
@james-w-macdonald-5106
Last seen 16 hours ago
United States

Ensembl 91 is just released, and with that the various mirrors can get behind the main site. You can force the use of the main site with the ensemblRedirect argument.

> library(biomaRt)
> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> getBM(c("hgnc_symbol"), "hgnc_symbol", "MLK2", mart= human)​
                                                                                                    <!DOCTYPE HTML PUBLIC -//IETF//DTD HTML 2.0//EN>
1                                                                                                                                       <html><head>
2                                                                                                                           <title>302 Found</title>
3                                                                                                                                      </head><body>
4                                                                                                                                     <h1>Found</h1>
5 <p>The document has moved <a href=//useast.ensembl.org/biomart/martservice?;redirectsrc=//www.ensembl.org%2Fbiomart%2Fmartservice%3F>here</a>.</p>
6                                                                                                                                     </body></html>
Warning message:
In .setResultColNames(result, mart = mart, attributes = attributes,  :
  Problems assigning column names.Currently using the biomart description field.You may wish to set these manually.

## re-run using ensemblRedirect=FALSE

> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", ensemblRedirect=FALSE)
>  getBM(c("hgnc_symbol"), "hgnc_symbol", "MLK2", mart= human)​
[1] hgnc_symbol
<0 rows> (or 0-length row.names)
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0
Entering edit mode

Or if we use a couple of symbols that exist:

> getBM("hgnc_symbol","hgnc_symbol", c("BRCA1","BRCA2"), human)
  hgnc_symbol
1       BRCA1
2       BRCA2
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0
Entering edit mode

I see the same error when I use the getLDS() function to get mouse homologs for human gene list.

getLDS(attributes = c("hgnc_symbol","chromosome_name", "start_position"), filters = "hgnc_symbol", values = "TP53", mart = human, 
    attributesL = c("chromosome_name","start_position"), martL = mouse)

In the middle of the message it reads as:

 <p>The document has moved <a href=//useast.ensembl.org/biomart/martservice?redirect=no?;redirectsrc=//www.ensembl.org%2Fbiomart%2Fmartservice%3Fredirect%3Dno%3F>here</a>.</p>

I tried ensemblRedirect=FALSE as well but no change.

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0
Entering edit mode

Please try with biomaRt version 2.35.2 available via:

BiocInstaller::biocLite('grimbough/biomaRt')

Then specify host = www.ensembl.org and ensemblRedirect = FALSE. There was still an issue with redirection that I have now patched.

I'm not exactly sure why it isn't working with the local mirrors, although I'm sure it is related to the Ensembl release yesterday, but using the main site works for me.

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0
Entering edit mode

I installed the new version and used the settings as you suggested. I still have the same issue. My session info is:

Session info ----------------------------------------------------------------
 setting  value                       
 version  R version 3.4.2 (2017-09-28)
 system   x86_64, mingw32             
 ui       RStudio (1.1.383)           
 language (EN)                        
 collate  English_United States.1252  
 tz       America/New_York            
 date     2017-12-13                  

Packages --------------------------------------------------------------------
 package       * version  date       source                            
 AnnotationDbi   1.40.0   2017-10-31 Bioconductor                      
 assertthat      0.2.0    2017-04-11 CRAN (R 3.4.2)                    
 base          * 3.4.2    2017-09-28 local                             
 Biobase         2.38.0   2017-10-31 Bioconductor                      
 BiocGenerics    0.24.0   2017-10-31 Bioconductor                      
 BiocInstaller   1.28.0   2017-10-31 Bioconductor                      
 biomaRt       * 2.35.2   2017-12-13 Github (grimbough/biomaRt@a221c7a)
 bit             1.1-12   2014-04-09 CRAN (R 3.4.1)                    
 bit64           0.9-7    2017-05-08 CRAN (R 3.4.1)                    
 bitops          1.0-6    2013-08-17 CRAN (R 3.4.1)                    
 blob            1.1.0    2017-06-17 CRAN (R 3.4.2)                    
 compiler        3.4.2    2017-09-28 local                             
 curl            3.1      2017-12-12 CRAN (R 3.4.2)                                 

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1
Entering edit mode

Ditto, still having the same issue, but only when running getLDS, not getBM

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1
Entering edit mode

I am also encountering this same error with getBM with and without ensemblRedirect = FALSE

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0
Entering edit mode

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.

 

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0
Entering edit mode
@romicakerketta-14630
Last seen 2.7 years ago

Hi everyone, try the following code. It is working perfectly fine for me right now. I am working with mouse data and if you are working with other species, just change the name to that of the species.

CODE:

BiocInstaller::biocLite('grimbough/biomaRt')
library(biomaRt)

listMarts(mart = NULL, host="www.ensembl.org", path="/biomart/martservice",
port=80, includeHosts = FALSE, archive = FALSE, ssl.verifypeer = TRUE,
ensemblRedirect = TRUE, verbose = FALSE)

ensembl = useEnsembl(biomart="ensembl", dataset="mmusculus_gene_ensembl")

transcript_ID <- biomaRt::getBM(attributes = c("ensembl_transcript_id_version", "ensembl_gene_id","external_gene_name"), mart = ensembl)
ADD COMMENT
1
Entering edit mode

getBM seems to work, but getLDS is not working still.

ADD REPLY
0
Entering edit mode

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.

 

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