Question

biomaRt error in getBM for hsapiens_gene_ensembl

1

Entering edit mode

rbacher ▴ 20

@rbacher-12895

Last seen 10 weeks ago

United States

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 • 3.8k views

ADD COMMENT • link updated 7.0 years ago by romicakerketta • 0 • written 7.0 years ago by rbacher ▴ 20

score 1 · Answer 1 · 2017-12-12

1

Entering edit mode

James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 2 days 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)

ADD COMMENT • link 7.0 years ago James W. MacDonald 67k

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

ADD REPLY • link 7.0 years ago James W. MacDonald 67k

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.

ADD REPLY • link 7.0 years ago sgupt46 ▴ 10

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.

ADD REPLY • link 7.0 years ago Mike Smith ★ 6.6k

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)

ADD REPLY • link 7.0 years ago sgupt46 ▴ 10

1

Entering edit mode

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

ADD REPLY • link 7.0 years ago michael.nagle ▴ 20

1

Entering edit mode

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

ADD REPLY • link 7.0 years ago lshepard ▴ 40

0

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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 REPLY • link 7.0 years ago Mike Smith ★ 6.6k

score 0 · Answer 2 · 2017-12-13

0

Entering edit mode

romicakerketta • 0

@romicakerketta-14630

Last seen 2.2 years ago

United States

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 • link 7.0 years ago romicakerketta • 0

1

Entering edit mode

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

ADD REPLY • link 7.0 years ago michael.nagle ▴ 20

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.

ADD REPLY • link 7.0 years ago Mike Smith ★ 6.6k