Question: Error in biomaRt query - "biomaRt expected a character string of length 1.
0
gravatar for benjaminbarnhart19
4 months ago by
benjaminbarnhart190 wrote:

I'm submitting a large query to Biomart, using the R package. The batch query was processing, made it about 38% of the way before throwing an error, which included "Please report this on the support site at http://support.bioconductor.org"

the full error message is here: "Error in getBM(attributes = c("entrezgeneaccession"), filters = c("externalgene_name"), : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this on the support site at http://support.bioconductor.org"

My code here: entz <- df$Gene.Symbol #a large vector of gene symbols zdEntz <- getBM(attributes = c('entrezgeneaccession'), filters = c('externalgenename'), values = list(entz, TRUE), mart = variation)

I'm running R version 3.6.0, with biomart_2.40.1

biomart R • 124 views
ADD COMMENTlink modified 4 months ago by Puks10 • written 4 months ago by benjaminbarnhart190

See this previous answer: https://support.bioconductor.org/p/121331/

Here is a copy paste from the reply from Mike Smith on that post:

It might be that the main Ensembl site is being a bit slow today. You can try querying one of the mirror sites e.g.

  mart <- useEnsembl(biomart = "ensembl", 
               dataset = "hsapiens_gene_ensembl", 
               mirror = "useast") Values for the mirror argument are: useast, uswest, asia.
  
ADD REPLYlink written 4 months ago by Puks10
Answer: Error in biomaRt query - "biomaRt expected a character string of length 1.
1
gravatar for Puks
4 months ago by
Puks10
Estonia
Puks10 wrote:

See this previous answer: https://support.bioconductor.org/p/121331/

Here is a copy paste from the reply from Mike Smith on that post:

It might be that the main Ensembl site is being a bit slow today. You can try querying one of the mirror sites e.g.

  mart <- useEnsembl(biomart = "ensembl", 
               dataset = "hsapiens_gene_ensembl", 
               mirror = "useast") Values for the mirror argument are: useast, uswest, asia.
  
ADD COMMENTlink written 4 months ago by Puks10
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