[BioC] Where to get BAM files for easyRNASeq human use case ALSO ANNOTATION
whuber at embl.de
Fri Aug 17 14:35:01 CEST 2012
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
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.
Martin Morgan scripsit 08/17/2012 02:16 PM:
> On 08/17/2012 04:36 AM, Steve Lianoglou wrote:
>> On Friday, August 17, 2012, Wolfgang Huber wrote:
>>> On 8/17/12 9:48 AM, Nicolas Delhomme wrote:
>> 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
> 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))
>  "GRangesList"
>  "GenomicRanges"
> the rowData is a GRangesList of length nrow(m), and with all ranges with
> length 0.
>> 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?
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