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

[Nicolas Delhomme]

Hi Wolfgang,

Can you please let me know once you've got it scheduled? The first deadline of the release 2.11 is in a month and I will add support for SummarizedExperiments in easyRNASeq by then. Changing its interface to DESeq/DEXSeq would not take long either, but it would be good to know whether this would be for 2.11 or 2.12.

Cheers,

Nico

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On Aug 17, 2012, at 2:35 PM, Wolfgang Huber wrote:

> 
> Hi Martin
> 
> thanks! I wasn't aware this worked now (and it wasn't immediately obvious when I tried this morning). So we can move ahead. I'll discuss with Simon and Alejandro about how to proceed (without major disruption or -traction)
> 
> Steve: you asked why. For DESeq, we have had applications e.g. with count data from mass spec (where there is sometimes no associated genomic interval), or from HiC (where there are typically two genomic intervals for each count). I'd like to keep the flexibility for dealing with these sorts of situations. And people might always have count tables where the coordinates were dropped - while not ideal, there is no reason why DE(X)Seq should refuse to work with these.
> 
> 	Best wishes
> 	Wolfgang
> 
> 
> 
> 
> Martin Morgan scripsit 08/17/2012 02:16 PM:
>> On 08/17/2012 04:36 AM, Steve Lianoglou wrote:
>>> 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.
>> 
>> I recently implemented support for no coordinates,
>> 
>> > m = matrix(0, 10, 5, dimnames=list(LETTERS[1:10], letters[1:5]))
>> > sx = SummarizedExperiment(m) ## etc;
>> > class(rowData(sx))
>> [1] "GRangesList"
>> attr(,"package")
>> [1] "GenomicRanges"
>> 
>> the rowData is a GRangesList of length nrow(m), and with all ranges with
>> length 0.
>> 
>> Martin
>> 
>>> 
>>> 
>>> 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
>>> 
>>> 
>>> 
>> 
>> 
> 
> 
> -- 
> Best wishes
> 	Wolfgang
> 
> Wolfgang Huber
> EMBL
> http://www.embl.de/research/units/genome_biology/huber
> 
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