Hi,
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
locale:
[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!
Raquel
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="uswest.ensembl.org", 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!
regards,
Aldo
> 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
locale:
[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
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.