Hi,

On Friday, August 17, 2012, Wolfgang Huber wrote:

>
>
> On 8/17/12 9:48 AM, Nicolas Delhomme wrote:


[snip]

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.


Interesting.

I'm trying to think of why this restriction doesn't make sense for DESeq
and co's count tables but I'm drawing a blank.

The counts in each row of the count table are surely coming from some
genomic locus, no?

Are you thinking about thing like gene fusion events or something?

Thanks,
-steve



-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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