Question: biomaRt error in getBM for hsapiens_gene_ensembl
1
gravatar for rbacher
20 months ago by
rbacher10
rbacher10 wrote:

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 • 1.1k views
ADD COMMENTlink modified 20 months ago by romicakerketta0 • written 20 months ago by rbacher10
Answer: biomaRt error in getBM for hsapiens_gene_ensembl
1
gravatar for James W. MacDonald
20 months ago by
United States
James W. MacDonald50k wrote:

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)
ADD COMMENTlink written 20 months ago by James W. MacDonald50k

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
ADD REPLYlink written 20 months ago by James W. MacDonald50k

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.

ADD REPLYlink modified 20 months ago • written 20 months ago by sgupt460

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.

ADD REPLYlink written 20 months ago by Mike Smith3.9k

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)                                 

ADD REPLYlink written 20 months ago by sgupt460
1

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

ADD REPLYlink written 20 months ago by michael.nagle20
1

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

ADD REPLYlink written 20 months ago by lshepard20

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 written 20 months ago by Mike Smith3.9k
Answer: biomaRt error in getBM for hsapiens_gene_ensembl
0
gravatar for romicakerketta
20 months ago by
romicakerketta0 wrote:

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 COMMENTlink modified 20 months ago • written 20 months ago by romicakerketta0
1

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

ADD REPLYlink written 20 months ago by michael.nagle20

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 written 20 months ago by Mike Smith3.9k
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