bioMaRt error : "BioMart webservice returned an invalid result: biomaRt expected a character string of length 1"
Entering edit mode
rdpinho • 0
Last seen 4.4 years ago


I am getting this error when I try to run bioMaRt on R.

Error in getBM(attributes = c("ensembl_transcript_id_version", "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.

I have used this code before multiple times including with the same dataset. 

here is the sessioninfo() and the code that I have used:

> library(biomaRt)
> mart<- useMart("ensembl")
> Pig_ensembl<- useDataset("sscrofa_gene_ensembl", mart=mart)

> head(row.names(DataMalFF_ile))
[1] "ENSSSCT00000040683.1" "ENSSSCT00000058261.1"
[3] "ENSSSCT00000002343.3" "ENSSSCT00000002323.3"
[5] "ENSSSCT00000037386.1" "ENSSSCT00000057714.1"
> tx2gene <-  getBM(attributes = c( "ensembl_transcript_id_version","ensembl_gene_id"), filters= "ensembl_transcript_id_version", values = row.names(DataMalFF_ile), mart = Pig_ensembl)

> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

[1] LC_COLLATE=Portuguese_Brazil.1252 
[2] LC_CTYPE=Portuguese_Brazil.1252   
[3] LC_MONETARY=Portuguese_Brazil.1252
[4] LC_NUMERIC=C                      
[5] LC_TIME=Portuguese_Brazil.1252    

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

other attached packages:
[1] biomaRt_2.36.0       edgeR_3.22.1        
[3] limma_3.36.1         BiocInstaller_1.30.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16         AnnotationDbi_1.42.1
 [3] xml2_1.2.0           magrittr_1.5        
 [5] knitr_1.20           progress_1.1.2      
 [7] IRanges_2.14.9       BiocGenerics_0.26.0 
 [9] bit_1.1-12           lattice_0.20-35     
[11] R6_2.2.2             httr_1.3.1          
[13] stringr_1.3.1        blob_1.1.1          
[15] tools_3.5.0          parallel_3.5.0      
[17] grid_3.5.0           Biobase_2.40.0      
[19] DBI_1.0.0            assertthat_0.2.0    
[21] yaml_2.1.19          bit64_0.9-7         
[23] digest_0.6.15        S4Vectors_0.18.1    
[25] bitops_1.0-6         curl_3.2            
[27] RCurl_1.95-4.10      memoise_1.1.0       
[29] RSQLite_2.1.1        stringi_1.2.2       
[31] compiler_3.5.0       prettyunits_1.0.2   
[33] stats4_3.5.0         XML_3.98-1.11       
[35] locfit_1.5-9.1      

I would really appreciate some resuolution to this problem. I have updated  all packages, inclusing bioMaRt and it didn't work.

Thank you!



r package problem • 2.6k views
Entering edit mode

I got similar problems and could get things to work by using an Ensembl mirror site and setting 'ensemblRedirect' to FALSE:

(I am in Europe, so by default the UK Sanger site)

> mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host="", ensemblRedirect = FALSE)

> annot.biomart = getBM(attributes = c("agilent_wholegenome", "entrezgene", "hgnc_symbol","description","ensembl_gene_id"), 
+                       filters = "agilent_wholegenome", values = MA.vsn.df$genes$ProbeName, mart = mart)

Hope this helps! 




> sessionInfo()

R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] biomaRt_2.34.2       GSEABase_1.40.1      graph_1.56.0         annotate_1.56.2      XML_3.98-1.11       
 [6] AnnotationDbi_1.40.0 IRanges_2.12.0       S4Vectors_0.16.0     Biobase_2.38.0       BiocGenerics_0.24.0 
[11] GSVA_1.26.0          limma_3.34.9        

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.16       compiler_3.4.3     later_0.7.2        RColorBrewer_1.1-2 prettyunits_1.0.2  progress_1.1.2    
 [7] bitops_1.0-6       tools_3.4.3        digest_0.6.15      bit_1.1-12         RSQLite_2.1.1      memoise_1.1.0     
[13] shiny_1.0.5        DBI_1.0.0          curl_3.2           httr_1.3.1         stringr_1.3.0      bit64_0.9-7       
[19] grid_3.4.3         R6_2.2.2           geneplotter_1.56.0 blob_1.1.1         magrittr_1.5       promises_1.0.1    
[25] htmltools_0.3.6    shinythemes_1.1.1  assertthat_0.2.0   mime_0.5           xtable_1.8-2       httpuv_1.4.2      
[31] stringi_1.2.2      RCurl_1.95-4.10

Entering edit mode

It's a good idea to tag you post with the name of the package you're trying to use - that way the author of the package gets an email notifying them that a question has been asked.  You should be able to edit your post to add the biomaRt tag.


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