Question

biomaRT getBM error

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scanchi • 0

@scanchi-14313

Last seen 6.7 years ago

Dear All,

I have used this code to query biomart database previously with no error.

mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                         dataset = "hsapiens_gene_ensembl",
                         host = 'ensembl.org')
mart
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the hsapiens_gene_ensembl dataset

mapping <- getBM(attributes = c("ensembl_gene_id", "ensembl_transcript_id"), mart = mart)

But now, I get two different errors:

mapping <- getBM(attributes = c("ensembl_gene_id","ensembl_transcript_id"), mart = mart)
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have 3 elements

mapping <- biomaRt::getBM(attributes = c("ensembl_gene_id","ensembl_transcript_id"), mart = mart)
No encoding supplied: defaulting to UTF-8.
Error in biomaRt::getBM(mart = mart, attributes = c("ensembl_transcript_id", : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

Is this related to the biomaRt connection issues that have been recently posted ?

sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.6 (Final)

Matrix products: default BLAS: /projects/builder-group/jpg/R-bioconductor/lib64/R/lib/libRblas.so LAPACK: /projects/builder-group/jpg/R-bioconductor/lib64/R/lib/libRlapack.so

locale: [1] C

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

other attached packages: [1] dplyr_0.7.4 biomaRt_2.34.1

biomart getbm ensembl • 2.1k views

ADD COMMENT • link updated 6.7 years ago by Mike Smith ★ 6.6k • written 6.7 years ago by scanchi • 0

score 0 · Answer 1 · 2018-03-02

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Mike Smith ★ 6.6k

@mike-smith

Last seen 7 hours ago

EMBL Heidelberg

This is the same issue seen in biomaRt getBM error in scan

For the host argument you need to explicitly put the 'www ', since there are many possible subdomains for ensembl.org e.g.

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

This has been patched in the developmental version of biomaRt.

ADD COMMENT • link 6.7 years ago Mike Smith ★ 6.6k

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Thank you Mike! That fixed the issue.

ADD REPLY • link 6.7 years ago scanchi • 0

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Hi Mike,

I am having the same issue. I get the following error:

"Error in getBM(attributes = c("hgnc_symbol", "ensembl_gene_id"), filters = "ensembl_gene_id", :
The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.".

My code is:

library(biomaRt)
listMarts()
ensembl <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl",
host = "www.ensembl.org",
path="/biomart/martservice")
ids=HLD$ensembl_gene_id
symbols = getBM(attributes = c("hgnc_symbol", "ensembl_gene_id"),
filters = "ensembl_gene_id",
values = ids,
mart = ensembl)

I have tried the code even without path function in useMart but keeps getting the same error.

Thank you for your help.

ADD REPLY • link 6.7 years ago sonal.gahlawat • 0

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On this site it's normally good practice to start a new question, rather than comment on an old one, they're much more likely to get noticed.

I can run your example without a problem, so can you post a new question and also include the output of the command `sessionInfo()`. This lets us see the versions of R and biomaRt that you are using.

ADD REPLY • link 6.7 years ago Mike Smith ★ 6.6k