Biomart has recently changed its server from www.biomart.org to www.ensembl.org
This leads to the following when loading the package:
> library(biomaRt)
> listEnsembl()
[1] biomart version
<0 rows> (or 0-length row.names)
>
a month ago everything was fine:
> listEnsembl()
biomart version
1 ensembl Ensembl Genes 84
2 snp Ensembl Variation 84
3 regulation Ensembl Regulation 84
4 vega Vega 64
I'm using biomaRt with easyRNASeq to annotate my RNA-Seq data.
A suggested workaround is:
listMarts(host = "www.ensembl.org")
but that doesn't work for me:
> listMarts(host='www.ensembl.org')
[1] biomart version
<0 rows> (or 0-length row.names)
What shall I do? This is quite frustrating. Session Info below. Do I need to upgrade to R 3.3 and biomart 2.28???
> sessionInfo()
R version 3.2.1 (2015-06-18)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.26.1 BiocInstaller_1.20.3
loaded via a namespace (and not attached):
[1] IRanges_2.4.8 parallel_3.2.1 DBI_0.4-1
[4] tools_3.2.1 RCurl_1.95-4.8 Biobase_2.30.0
[7] AnnotationDbi_1.32.3 RSQLite_1.0.0 S4Vectors_0.8.11
[10] BiocGenerics_0.16.1 stats4_3.2.1 bitops_1.0-6
[13] XML_3.98-1.4
