Question: Biomart error: Does anyone know how to solve this error?
0
gravatar for star
19 months ago by
star190
Netherlands
star190 wrote:
> head(data)

 ID adj.    P.Val   P.Value  logFC     SPOT_ID Gene.Symbol
1 39846     0.998 0.0000870 -1.070 A_73_114228   LOC511158
2 13443     0.998 0.0000982 -0.504 A_73_111136    BI542041
3 30457     0.998 0.0001036  0.450 A_73_111981   LOC508459
4  2720     0.998 0.0001282 -0.437               
5 18021     0.998 0.0002285 -0.388 A_73_113953   LOC614467
6 25665     0.998 0.0002665  0.321 A_73_115472   LOC530858

> mart1<- useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="btaurus_gene_ensembl", host="www.ensembl.org")
> mart2 <- getBM(attributes='ensembl_gene_id', filters='external_gene_name',  values=data$Gene.Symbol, mart=mart1)
Error in getBM(attributes = "ensembl_gene_id", filters = "external_gene_name",  : 
  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.

> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252     LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
[1] biomaRt_2.18.0       BiocInstaller_1.12.1

loaded via a namespace (and not attached):
[1] bitops_1.0-6   RCurl_1.95-4.5 tools_3.0.2    XML_3.98-1.1
ensembl biomart R genome • 818 views
ADD COMMENTlink modified 19 months ago by Denise - Open Targets5.0k • written 19 months ago by star190

Please use a more informative title to let people know what the post is about before they decide to open it. Even a simple "BioMart error" would do compared to what is there now.

ADD REPLYlink modified 19 months ago • written 19 months ago by genomax71k

Are you running latest version of biomaRt? That is generally the first thing to check. People will likely ask for sessionInfo() so go ahead and add that to your post as well.

ADD REPLYlink written 19 months ago by genomax71k
0
gravatar for Denise - Open Targets
19 months ago by
UK, Hinxton, EMBL-EBI
Denise - Open Targets5.0k wrote:

I think the choice of filters (i.e. external_gene_name) is wrong. The LOC is a NCBI gene name. Leave the LOC out and use the numbers only to get NCBI gene ID. LOC511158 is the gene name and 511158 is the NCBI gene ID you should select/input in BioMart.

Note that out of the NCBI IDs above I could only find the ENSG IDs for 511158 (ENSBTAG00000009599) and 614467 (ENSBTAG00000021432) using BioMart.

Are you sure the other LOC IDs are still standing? Some of the LOCs get other names now e.g. 614467 is NCBI gene name TEDDM1 now.

ADD COMMENTlink modified 19 months ago • written 19 months ago by Denise - Open Targets5.0k
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