Question

BiomaRt getBM Error when converting from Ensemble to RNACentral IDs

0

Entering edit mode

Michael • 0

@51461f2d

Last seen 3.6 years ago

United States

I'm trying to convert a list of Ensemble gene IDs to RNACentral Gene IDs using BiomaRt, but I'm not very experienced with R. My code is

library(biomaRt)

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

tx <- scan('R/test_study.txt', character(), quote = "")
tx <- strsplit(tx, "\" \"")


res <- getBM(
  attributes = c("rnacentral"),
  filters = "ensembl_gene_id_version",
  values = tx,
  mart = mart)

I'm getting this error:

Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery,  : 
  Query ERROR: caught BioMart::Exception::Usage: Filter NA NOT FOUND

Session Info

R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

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_2.46.3

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6           pillar_1.6.0         compiler_4.0.3       BiocManager_1.30.12  dbplyr_2.1.1        
 [6] prettyunits_1.1.1    tools_4.0.3          progress_1.2.2       bit_4.0.4            tibble_3.1.1        
[11] RSQLite_2.2.7        memoise_2.0.0        BiocFileCache_1.14.0 lifecycle_1.0.0      pkgconfig_2.0.3     
[16] rlang_0.4.11         DBI_1.1.1            curl_4.3.1           parallel_4.0.3       fastmap_1.1.0       
[21] withr_2.4.2          dplyr_1.0.5          stringr_1.4.0        httr_1.4.2           xml2_1.3.2          
[26] rappdirs_0.3.3       generics_0.1.0       S4Vectors_0.28.1     vctrs_0.3.7          askpass_1.1         
[31] IRanges_2.24.1       hms_1.0.0            tidyselect_1.1.1     stats4_4.0.3         bit64_4.0.5         
[36] glue_1.4.2           Biobase_2.50.0       R6_2.5.0             fansi_0.4.2          AnnotationDbi_1.52.0
[41] XML_3.99-0.6         purrr_0.3.4          blob_1.2.1           magrittr_2.0.1       ellipsis_0.3.1      
[46] BiocGenerics_0.36.1  assertthat_0.2.1     utf8_1.2.1           stringi_1.5.3        openssl_1.4.4       
[51] cachem_1.0.4         crayon_1.4.1

biomaRt • 1.9k views

ADD COMMENT • link written 3.6 years ago by Michael • 0

0

Entering edit mode

Can you give some examples of the content of tx maybe via head(tx)?

Errors of the form caught BioMart::Exception::Usage: Filter NA NOT FOUND are from the Ensembl server rather than the R package, but it's hard to suggest why without knowing what values are being sent to it.

ADD REPLY • link 3.6 years ago Mike Smith ★ 6.6k

0

Entering edit mode

Trying again today with the same code, it's actually showing a different error now.

Loading required package: biomaRt
> library(biomaRt)
> mart <- useEnsembl(biomart = "ensembl", 
+                    dataset = "hsapiens_gene_ensembl", 
+                    mirror = "useast")
Ensembl site unresponsive, trying www mirror
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [useast.ensembl.org:8443] Connection timed out after 10001 milliseconds
> tx <- scan('R/test_study.txt', character(), quote = "")
Read 14763 items
> tx <- strsplit(tx, "\" \"")
> res <- getBM(
+   attributes = c("rnacentral"),
+   filters = "ensembl_gene_id_version",
+   values = tx,
+   mart = mart)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: [useast.ensembl.org:8443] Connection timed out after 10004 milliseconds

Here is the head(tx)

> head(tx)
[[1]]
[1] "ENSG00000242268.2"

[[2]]
[1] "ENSG00000270112.3"

[[3]]
[1] "ENSG00000167578.15"

[[4]]
[1] "ENSG00000078237.5"

[[5]]
[1] "ENSG00000146083.10"

[[6]]
[1] "ENSG00000225275.4"

ADD REPLY • link 3.6 years ago Michael • 0

0

Entering edit mode

Nevermind, it now always returns the original error, I'm not sure why it was showing a new error for a little while.

ADD REPLY • link 3.6 years ago Michael • 0

score 2 · Answer 1 · 2021-05-03

> tx <- list("ENSG00000242268.2","ENSG00000270112.3","ENSG00000167578.1","ENSG00000078237.5","ENSG00000146083.10","ENSG00000225275.4")
> tx
[[1]]
[1] "ENSG00000242268.2"

[[2]]
[1] "ENSG00000270112.3"

[[3]]
[1] "ENSG00000167578.1"

[[4]]
[1] "ENSG00000078237.5"

[[5]]
[1] "ENSG00000146083.10"

[[6]]
[1] "ENSG00000225275.4"

> getBM("rnacentral","ensembl_gene_id_version", tx, mart)
Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery,  : 
  Query ERROR: caught BioMart::Exception::Usage: Filter NA NOT FOUND
> getBM("rnacentral","ensembl_gene_id_version", unlist(tx), mart)
     rnacentral
1 URS00008C229F

The values argument is supposed to be a vector, not a list.

score 0 · Answer 2 · 2021-05-04

tx <- list("ENSG00000242268.2","ENSG00000270112.3","ENSG00000167578.1","ENSG00000078237.5","ENSG00000146083.10","ENSG00000225275.4") tx 1 "ENSG00000242268.2"

[2] "ENSG00000270112.3"

[3] "ENSG00000167578.1"

[4] "ENSG00000078237.5"

[5] "ENSG00000146083.10"

[6] "ENSG00000225275.4"

getBM("rnacentral","ensembl_gene_id_version", tx, mart) Error in .processResults(postRes, mart = mart, sep = sep, fullXmlQuery = fullXmlQuery, : Query ERROR: caught BioMart::Exception::Usage: Filter NA NOT FOUND getBM("rnacentral","ensembl_gene_id_version", unlist(tx), mart) rnacentral 1 URS00008C229F

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