Error when retrieving gene name data using biomaRt
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Entering edit mode
@ericayscott-20490
Last seen 5.0 years ago

I continue to get this error when trying to use biomaRt: my code: Genenames <- gsessionInfo()etBM(attributes=c('ensemblgeneidversion', 'ensemblgeneid','externalgenename'), filters = 'ensemblgeneidversion', values = EIds, mart = ensemblmart95) resulting error: Batch submitting query [===>--------------------------------------] 10% eta: 31sError in getBM(attributes = c("ensemblgeneidversion", "ensemblgene_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

sessionInfo() R version 3.5.0 (2018-04-23) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: macOS 10.14

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale: [1] enCA.UTF-8/enCA.UTF-8/enCA.UTF-8/C/enCA.UTF-8/en_CA.UTF-8

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

other attached packages: [1] WGCNA1.66 fastcluster1.1.25 dynamicTreeCut1.63-1 [4] ggExtra0.8 viridis0.5.1 viridisLite0.3.0
[7] ggplot23.1.0 biomaRt2.38.0 edgeR3.24.3
[10] limma
3.38.3 reshape0.8.8 dplyr0.7.8
[13] plyr1.8.4 reshape21.4.3

loaded via a namespace (and not attached): [1] bitops1.0-6 matrixStats0.54.0 fit.models0.5-14
[4] robust
0.4-18 bit640.9-7 doParallel1.0.14
[7] RColorBrewer1.1-2 progress1.2.0 httr1.4.0
[10] backports
1.1.3 tools3.5.0 R62.3.0
[13] rpart4.1-13 Hmisc4.2-0 DBI1.0.0
[16] lazyeval
0.2.1 BiocGenerics0.28.0 colorspace1.4-0
[19] nnet7.3-12 withr2.1.2 tidyselect0.2.5
[22] gridExtra
2.3 prettyunits1.0.2 preprocessCore1.44.0 [25] bit1.1-14 curl3.3 compiler3.5.0
[28] Biobase
2.42.0 htmlTable1.13.1 xml21.2.0
[31] labeling0.3 checkmate1.9.1 scales1.0.0
[34] mvtnorm
1.0-8 DEoptimR1.0-8 robustbase0.93-3
[37] stringr1.3.1 digest0.6.18 foreign0.8-71
[40] rrcov
1.4-7 base64enc0.1-3 pkgconfig2.0.2
[43] htmltools0.3.6 htmlwidgets1.3 rlang0.3.1
[46] impute
1.56.0 rstudioapi0.9.0 RSQLite2.1.1
[49] shiny1.2.0 bindr0.1.1 acepack1.4.1
[52] RCurl
1.95-4.11 magrittr1.5 GO.db3.7.0
[55] Formula1.2-3 Matrix1.2-15 Rcpp1.0.0
[58] munsell
0.5.0 S4Vectors0.20.1 stringi1.2.4
[61] MASS7.3-51.1 grid3.5.0 blob1.1.1
[64] parallel
3.5.0 promises1.0.1 crayon1.3.4
[67] miniUI0.1.1.1 lattice0.20-38 splines3.5.0
[70] hms
0.4.2 locfit1.5-9.1 knitr1.21
[73] pillar1.3.1 codetools0.2-16 stats43.5.0
[76] XML
3.98-1.16 glue1.3.0 latticeExtra0.6-28
[79] data.table1.12.0 httpuv1.4.5.1 foreach1.4.4
[82] gtable
0.2.0 purrr0.3.0 assertthat0.2.0
[85] xfun0.4 mime0.6 xtable1.8-3
[88] later
0.7.5 pcaPP1.9-73 survival2.43-3
[91] tibble2.0.1 iterators1.0.10 AnnotationDbi1.44.0 [94] memoise1.1.0 IRanges2.16.0 bindrcpp0.2.2
[97] cluster_2.0.7-1

software error annotation Biomart • 408 views
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Entering edit mode
Mike Smith ★ 6.5k
@mike-smith
Last seen 18 hours ago
EMBL Heidelberg

I think Ensembl is currently experiencing some slowdown with their website, leading to a few reports of this in the past couple of days. You can try using a mirror as suggested in https://support.bioconductor.org/p/119983/

However, from your variable names it suggests you're using the Ensembl archive for version 95, so mirror site won't exist.

Given this and the fact you seem require bulk conversion of large numbers of IDs, it may be more efficient in the long term to use an ensembldb annotation package instead, or experiment with the Ensembl RestAPI which seems a little faster in my experience.

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