Error in biomaRt
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giotto_gui • 0
@giotto_gui-22568
Last seen 4.8 years ago

When I use "getBM" of biomaRt package to convert my gene ID, it displayed error reprot as follow:

Error in getBM (attributes = c("ensembl_gene_id", "entrezgene_id", "hgnc_symbol"),  : 
  The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. 

Does biomaRt not support multiple IDs matches now?

annotation • 672 views
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Can you provide an example of the code you're running, along with the output of sessionInfo()?

biomRt should work fine with multiple IDs, this is probably a server side error. The error message most likely indicates it got back nothing (a vector of length 0) rather than something - admittedly that's not at all clear.

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Hi, just chiming in here. I am also experiencing the same issue. I have input of the format

>head(tx2gene, 2)
              TXNAME             GENEID
1 ENSMMUT00000051915 ENSMMUG00000036181
2 ENSMMUT00000000911 ENSMMUG00000000634

Here's what I'm running:

library(biomaRt)
ensembl = useMart("ensembl", dataset="mmulatta_gene_ensembl")
converted = getBM(filters="ensembl_gene_id", attributes="hsapiens_homolog_ensembl_gene", values=tx2gene$GENEID, bmHeader=T, mart=ensembl)

Notably this works on a short test list of IDs, but if I try to convert all, I also get the error posted above, as well as a prompt to post on the forum here. Thanks any help.

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS

Matrix products: default
BLAS:   /afs/genomecenter.ucdavis.edu/software/R/3.6.1/lssc0-linux/lib/R/lib/libRblas.so
LAPACK: /afs/genomecenter.ucdavis.edu/software/R/3.6.1/lssc0-linux/lib/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US
 [4] LC_COLLATE=en_US     LC_MONETARY=en_US    LC_MESSAGES=en_US
 [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C
[10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.3                  compiler_3.6.1
 [3] pillar_1.4.2                GenomeInfoDb_1.20.0
 [5] XVector_0.24.0              GenomicFeatures_1.36.4
 [7] prettyunits_1.0.2           bitops_1.0-6
 [9] tools_3.6.1                 zlibbioc_1.30.0
[11] progress_1.2.2              zeallot_0.1.0
[13] biomaRt_2.40.5              digest_0.6.23
[15] bit_1.1-14                  lattice_0.20-38
[17] RSQLite_2.1.2               memoise_1.1.0
[19] tibble_2.1.3                pkgconfig_2.0.3
[21] rlang_0.4.2                 Matrix_1.2-17
[23] DelayedArray_0.10.0         DBI_1.0.0
[25] parallel_3.6.1              GenomeInfoDbData_1.2.1
[27] rtracklayer_1.44.3          httr_1.4.1
[29] stringr_1.4.0               Biostrings_2.52.0
[31] S4Vectors_0.22.1            vctrs_0.2.0
[33] IRanges_2.18.2              hms_0.5.1
[35] grid_3.6.1                  stats4_3.6.1
[37] bit64_0.9-7                 Biobase_2.44.0
[39] R6_2.4.1                    AnnotationDbi_1.46.1
[41] BiocParallel_1.18.1         XML_3.98-1.20
[43] blob_1.2.0                  magrittr_1.5
[45] matrixStats_0.55.0          GenomicAlignments_1.20.1
[47] Rsamtools_2.0.2             backports_1.1.5
[49] BiocGenerics_0.30.0         GenomicRanges_1.36.1
[51] SummarizedExperiment_1.14.1 assertthat_0.2.1
[53] stringi_1.4.3               RCurl_1.95-4.12
[55] crayon_1.3.4
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swbarnes2 ★ 1.4k
@swbarnes2-14086
Last seen 2 hours ago
San Diego

I get those as well. I get that when I'm submitting a large query, I've even gotten it when I'm submitting lots of small queries. I've changed the mirror it goes to, different database versions...As far as I can tell, you just have to resubmit until it goes to completion.

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@kerenyifarkas-22585
Last seen 4.8 years ago

I've also had the same issue. Just checked again and now it seems to be working fine.

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