Ensembl ids to gene symbol: Error The query to the BioMart webservice returned an invalid result

[Sanjeev Sariya]

hi All,

I'm trying to get mapped gene symbol to a list of ENSEMBL Ids i've. 

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.

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

##run code  
G_list <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id","hgnc_symbol"), values=genersem$gene_ID,mart= mart)
##

I'm using following platform and R packages:

BLAS: /mnt/mfs/cluster/bin/R-3.4/lib/libRblas.so
LAPACK: /mnt/mfs/cluster/bin/R-3.4/lib/libRlapack.so
other attached packages:
[1] biomaRt_2.34.2

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1           AnnotationDbi_1.42.1 xml2_1.2.0
 [4] magrittr_1.5         BiocGenerics_0.24.0  hms_0.4.2
 [7] progress_1.2.0       IRanges_2.12.0       bit_1.1-14
[10] R6_2.4.0             rlang_0.3.3          httr_1.4.0
[13] stringr_1.4.0        blob_1.1.1           tools_3.4.2
[16] parallel_3.4.2       Biobase_2.38.0       DBI_1.0.0
[19] bit64_0.9-7          digest_0.6.18        assertthat_0.2.1
[22] crayon_1.3.4         S4Vectors_0.16.0     bitops_1.0-6
[25] curl_3.3             RCurl_1.95-4.12      memoise_1.1.0
[28] RSQLite_2.1.1        stringi_1.4.3        compiler_3.4.2
[31] prettyunits_1.0.2    stats4_3.4.2         XML_3.98-1.19
[34] pkgconfig_2.0.2

Let me know if I can circumvent this anyhow.

Thanks!

[Syed Haider]

Hi Sanjeev,

Not sure whether it was but one thing i couldnt see in your code is your genersem$gene_ID.

Here is an equivalent (but modified gene.id variable) example that works on my end:

library(biomaRt);

mart<-useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = 

"www.ensembl.org", ensemblRedirect = FALSE);

gene.ids <- c("ENSG00000284532", "ENSG00000238933", "ENSG00000275693");

G_list <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id","hgnc_symbol"), values=gene.ids, mart= mart)

Best,

Syed

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[Sanjeev Sariya]

Dear Haider,

Thanks for looking into it.

The code works fine, say if I provide 10-20 ensembl gene ids. It starts honking with current list of ensembl ids I've, which is 50K+.

G_list <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id","hgnc_symbol"),  values=head(df$gene_ID),mart= mart)

It works fine with above code. If I remove head, I get error:

Batch submitting query [>------------------------------]   3% eta:  1hError in getBM(filters = "ensembl_gene_id", attributes = c("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.

--Sanjeev

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[Syed Haider]

Hi Sanjeev,

50K+ ids in the same query are perhaps too many. Worth sending multiple queries (sequentially) with smaller list of ids e.g 500 each!

Best,

Syed

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