GEO Download - "The query to BioMart webservice returned an invalid result..."
1
0
Entering edit mode
wes ▴ 10
@wes-16643
Last seen 2.3 years ago

I am attempting to download some data from GEO using the getBM() function from the biomaRt package. I am downloading multiple different GEO accessions, and some of them give the following error:

  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

Here is an example:

### Dependencies
library(GEOquery)
library(Biobase)
library(biomaRt)

### Set up Mart
mart <- useMart('ENSEMBL_MART_ENSEMBL')
mart <- useDataset('hsapiens_gene_ensembl', mart)

### Get sets (returns list of two ExpressionSets)
gset_ls <- getGEO("GSE4922", GSEMatrix = T, getGPL = F)
names(gset_ls)

[1] "GSE4922-GPL96_series_matrix.txt.gz" "GSE4922-GPL97_series_matrix.txt.gz"

### Select first one
myGSET <- gset_ls$GSE4922-GPL96_series_matrix.txt.gz

### Get annotation lookup
myLookup <- getBM(mart = mart, 
                  attributes = c("affy_hg_u133a", "ensembl_gene_id", "external_gene_name"), 
                  filter = "affy_hg_u133a",
                  values = rownames(exprs(myGSET)),
                  uniqueRows = T)

The getBM() function begins the download and works for a while, but then ends with:

Batch submitting query [=======================>----]  84% eta:  1mError in biomaRt::getBM(mart = mart, attributes = c("affy_hg_u133a, "ensembl_gene_id",  : 
  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

This exact same method works for other GEO accession numbers and arrays, only some accessions give this error. For example, using the GEO accession "GSE19615" and the GPL of "GPL570". This accession uses a different array, so the filter is "affy_hg_u133_plus_2"

GEO = "GSE19615"
GPL = "GPL570"
FILTER = "affy_hg_u133_plus_2

Session Info:

R version 3.6.0 (2019-04-26)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] readxl_1.3.1          wrh.rUtils_0.0.0.9000 data.table_1.12.2    
[4] biomaRt_2.40.0        GEOquery_2.52.0       usethis_1.5.0        
[7] devtools_2.0.2        Biobase_2.44.0        BiocGenerics_0.30.0  

loaded via a namespace (and not attached):
 [1] progress_1.2.2       tidyselect_0.2.5     remotes_2.0.4       
 [4] purrr_0.3.2          stats4_3.6.0         blob_1.1.1          
 [7] XML_3.98-1.20        rlang_0.3.4          pkgbuild_1.0.3      
[10] pillar_1.4.1         glue_1.3.1           withr_2.1.2         
[13] DBI_1.0.0            bit64_0.9-7          sessioninfo_1.1.1   
[16] stringr_1.4.0        cellranger_1.1.0     memoise_1.1.0       
[19] callr_3.2.0          IRanges_2.18.1       ps_1.3.0            
[22] curl_3.3             AnnotationDbi_1.46.0 Rcpp_1.0.1          
[25] readr_1.3.1          backports_1.1.4      BiocManager_1.30.4  
[28] limma_3.40.2         desc_1.2.0           S4Vectors_0.22.0    
[31] pkgload_1.0.2        fs_1.3.1             bit_1.1-14          
[34] hms_0.4.2            digest_0.6.19        stringi_1.4.3       
[37] processx_3.3.1       dplyr_0.8.1          rprojroot_1.3-2     
[40] cli_1.1.0            tools_3.6.0          bitops_1.0-6        
[43] magrittr_1.5         RCurl_1.95-4.12      tibble_2.1.3        
[46] RSQLite_2.1.1        crayon_1.3.4         tidyr_0.8.3         
[49] pkgconfig_2.0.2      xml2_1.2.0           prettyunits_1.0.2   
[52] assertthat_0.2.1     httr_1.4.0           rstudioapi_0.10     
[55] R6_2.4.0             compiler_3.6.0      
biomart geo software error ensembl • 376 views
ADD COMMENT
2
Entering edit mode
Mike Smith ★ 5.1k
@mike-smith
Last seen 2 hours ago
EMBL Heidelberg / de.NBI

You can try querying one of the Ensembl mirrors which may be more responsive for you e.g.

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl", 
                   mirror = "useast")

Values for the mirror argument are: useast, uswest, asia

ADD COMMENT
1
Entering edit mode

That worked great. Thanks, Mike!

ADD REPLY

Login before adding your answer.

Traffic: 312 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6