Good Morning,
I am trying to use Biomart to annotate genes but I always have this error message that appears :
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.
I find a subject on bioconductor about this issue : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query
But the error remains when I try to install a patched version via GitHub:
BiocInstaller::biocLite('grimbough/biomaRt')
And the code doesn't work when I try an archive version :
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", "http://Aug2017.archive.ensembl.org")
Error in listMarts(host = host, path = path, port = port, includeHosts = TRUE, :
Unexpected format to the list of available marts.
Please check the following URL manually, and try ?listMarts for advice.
http://Aug2017.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
here is the code I use :
require(biomaRt)
listMarts()
ensMart<-useMart("ensembl")
View(listDatasets(ensMart))
ensembl_hs_mart <- useMart(biomart="ensembl", dataset="mmusculus_gene_ensembl")
View(listAttributes(ensembl_hs_mart))
infos_genes = getBM(attributes=c("entrezgene"),mart = ensembl_hs_mart)
View(infos_genes)
infos_genes = getBM(attributes=c("entrezgene","percentage_gene_gc_content","gene_biotype","chromosome_name"),
filter="entrezgene",
values=rownames(countsTable),
mart = mart)
View(infos_genes)
session info :
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used (Mb) gc trigger (Mb) max used (Mb)
Ncells 449007 24.0 750400 40.1 592000 31.7
Vcells 804975 6.2 1650153 12.6 949924 7.3
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 4.3
year 2017
month 11
day 30
svn rev 73796
language R
version.string R version 3.4.3 (2017-11-30)
nickname Kite-Eating Tree
Memory set to 7839 Mb.
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R version 3.4.3 (2017-11-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 LC_MONETARY=French_France.1252
[4] LC_NUMERIC=C LC_TIME=French_France.1252
attached base packages:
[1] stats4 splines parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.34.2 EDASeq_2.12.0
[3] ShortRead_1.36.0 GenomicAlignments_1.14.1
[5] SummarizedExperiment_1.8.1 DelayedArray_0.4.1
[7] matrixStats_0.53.0 Rsamtools_1.30.0
[9] Biostrings_2.46.0 XVector_0.18.0
[11] BiocParallel_1.12.0 edgeR_3.20.7
[13] limma_3.34.6 Mus.musculus_1.3.1
[15] TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0 org.Mm.eg.db_3.5.0
[17] GO.db_3.5.0 OrganismDbi_1.20.0
[19] GenomicFeatures_1.30.3 GenomicRanges_1.30.0
[21] GenomeInfoDb_1.14.0 AnnotationDbi_1.40.0
[23] IRanges_2.12.0 S4Vectors_0.16.0
[25] NOISeq_2.22.0 Matrix_1.2-12
[27] Biobase_2.38.0 BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.15 locfit_1.5-9.1 lattice_0.20-35 prettyunits_1.0.2
[5] assertthat_0.2.0 digest_0.6.15 R6_2.2.2 aroma.light_3.8.0
[9] DESeq_1.30.0 RSQLite_2.0 httr_1.3.1 BiocInstaller_1.28.0
[13] pillar_1.2.1 zlibbioc_1.24.0 rlang_0.2.0 progress_1.1.2
[17] annotate_1.56.1 blob_1.1.0 R.utils_2.6.0 R.oo_1.21.0
[21] RMySQL_0.10.14 geneplotter_1.56.0 stringr_1.3.0 RCurl_1.95-4.10
[25] bit_1.1-12 compiler_3.4.3 rtracklayer_1.38.3 pkgconfig_2.0.1
[29] tibble_1.4.2 GenomeInfoDbData_1.0.0 XML_3.98-1.10 bitops_1.0-6
[33] R.methodsS3_1.7.1 grid_3.4.3 RBGL_1.54.0 xtable_1.8-2
[37] DBI_0.8 magrittr_1.5 graph_1.56.0 stringi_1.1.6
[41] genefilter_1.60.0 hwriter_1.3.2 latticeExtra_0.6-28 RColorBrewer_1.1-2
[45] tools_3.4.3 bit64_0.9-7 survival_2.41-3 yaml_2.1.17
[49] memoise_1.1.0 knitr_1.20
Thanks a lot,
Have a good day
I can run your example code fine, so I wonder if this is an issue with your internet connection.
What do you see if you go to http://Aug2017.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt in your web browser?
You should see some XML starting with
<MartRegistry>
If you see anything else then something unexpected is going on with your connection to Ensembl.