[BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION

[Wolfgang Huber]

On 8/17/12 9:48 AM, Nicolas Delhomme wrote:
> Martin - how standardized has the SummarizedExperiment class become?
> I suppose it is what I should be using for that purpose, right? One
> constraint I would have is that I need to generate an output that can
> easily be re-used by downstream analyses tool such as edgeR, DESeq,
> DEXSeq,... Do you know of any effort on migrating these "proprietary"
> object structures towards a common one?

We'd be happy to add methods or converters from SummarizedExperiment to
DESeq's CountDataSet and DEXSeq's ExonCountSet classes, presumably into 
these packages.

The problem is the reverse direction: SummarizedExperiment insists on 
having (non-NA) ranges information (start, end, width), while this is 
not a restriction that would make sense to impose on count tables for 
DESeq or DEXSeq.

Best wishes
	Wolfgang

Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber