Re: [Bioc-devel] Gene annotation: TxDb vs ENSEMBL/NCBI inconsistency

2015-06-08 Thread Rainer Johannes
dear Robert and Ludwig, the EnsDb packages provide all the gene/transcript etc annotations for all genes defined in the Ensembl database (for a given species and Ensembl release). Except the column/attribute "entrezid" that is stored in the internal database there is however no link to NCBI or

Re: [Bioc-devel] Changes in AnnotationDbi

2015-06-08 Thread James W. MacDonald
Thanks Marc! On Mon, Jun 8, 2015 at 3:12 PM, Marc Carlson wrote: > OK Jim, > > I will put very simple messages in (one liners) that will simply state > whether the relationship between keys and the requested columns was 1:1, > 1:many, many:1, or many:many. Hopefully this will represent an acc

Re: [Bioc-devel] Changes in AnnotationDbi

2015-06-08 Thread Marc Carlson
OK Jim, I will put very simple messages in (one liners) that will simply state whether the relationship between keys and the requested columns was 1:1, 1:many, many:1, or many:many. Hopefully this will represent an acceptable compromise. Marc On 06/05/2015 08:37 AM, James W. MacDonald wr

Re: [Bioc-devel] GSEABase::getOBOCollection() missing children

2015-06-08 Thread Robert Castelo
hi Martin, thanks for the quick fix!!! best regards, robert. On 06/05/2015 08:05 PM, Martin Morgan wrote: On 06/05/2015 08:51 AM, Robert Castelo wrote: hi, importing an OBO file with GSEABase::getOBOCollection() I have observed missing children in the imported ontology. Here is an example w