Closed lmsimp closed 9 years ago
Selecting 16 UniProt/Swissprot Accession(s) for human and mouse work fine when R is called from command line but not in RStudio?
@lmsimp please install again from github (still verion 1.9.1). It should work now.
Thank you very much for sorting this.
On 24 Apr 2015, at 03:29, Laurent Gatto notifications@github.com wrote:
@lmsimp please install again from github (still verion 1.9.1). It should work now.
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For the record, new marts are:
CHANGES IN VERSION 1.9.1
------------------------
o new plot2Ds function to overlay two data sets on the same PCA plot
[2015-04-17 Fri]
o regenerate biomart data used by setAnnotationParams
[2015-04-24 Fri]
## biomart version
## 1 ensembl ENSEMBL GENES 79 (SANGER UK)
## 5 fungi_mart_26 ENSEMBL FUNGI 26 (EBI UK)
## 7 metazoa_mart_26 ENSEMBL METAZOA 26 (EBI UK)
## 9 plants_mart_26 ENSEMBL PLANTS 26 (EBI UK)
old ones were biomart
(previous ENSEMBL GENES ??), fungi_mart_25
, metazoa_mart_25
and plants_mart_25
.
Fails for:
13: Arabidopsis thaliana genes (TAIR10 (2010-09-TAIR10)) 13: UniProtKB/SwissProt ID(s)
66: Drosophila melanogaster genes (BDGP5) 17: UniProt/Swissprot Accession(s) [e.g. P08111]
95: Homo sapiens genes (GRCh38) 15: UniProt/Swissprot Accession(s) [e.g. Q13068] but this works 16: UniProt/Swissprot ID(s) [e.g. Q9H3N8]
120: Mus musculus genes (GRCm38.p3) 15: UniProt/Swissprot Accession(s) [e.g. Q8K2Q7] but this works 16: UniProt/Swissprot ID(s) [e.g. P03888]