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lgatto / pRoloc

A unifying bioinformatics framework for organelle proteomics
http://lgatto.github.io/pRoloc/
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updating marts [was getAnnotationParams() failing] #50

Closed lmsimp closed 9 years ago

lmsimp commented 9 years ago

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]

lmsimp commented 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?

lgatto commented 9 years ago

@lmsimp please install again from github (still verion 1.9.1). It should work now.

lmsimp commented 9 years ago

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.

— Reply to this email directly or view it on GitHub.

lgatto commented 9 years ago

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.