On Fri, Sep 21, 2012 at 7:09 AM, Kasper Daniel Hansen <
kasperdanielhansen@gmail.com> wrote:

> So I think we need something like a list of SummarizedExperiments,
>

yes



> perhaps with a joint sampleData (how a joint sample data is mapped to
> multiple assays will need to be thought about).


yes



>  We might also have a
> joint GRanges which signifies "this is the region(s) we have data on",
> but we should still retain the individual ranges for each experiment.
>

this gets ugly fast, especially if you have bis-seq or eRRBS involved, but
to each his own

personally I have been delegating individual assays via .ShallowData from a
master container, which (once upon a time) contained a bunch of sub-assays
with defined slots, but eventually turned into a blobby type of structure
that only really handles colData (per-subject) and references to child
SummarizedExperiments, which aren't supposed to ever have their own
colData, just rowData and assays.  Making that work has taken longer than
I'd like



> Something like
>
> dataRanges
>   A GRanges, just telling up what is essentially the union of the
> rowData in the SummarizedExperiment below, or perhaps bigger.
> copyNumber
>   SummarizedExperiment, 3 samples
>   has assays "copyNumber" and perhaps "control"
> TF binding
>   SummarizedExperiment, 10 samples
>   has assays "TF1", .., "TF5" and "input"
>

fine although sometimes I suspect it's better to have raw RNAseq, BSseq,
DNAseq and then subset by ChIPseq results or 5C or whatever to look at
differences.  but that's just my bias, using TCGA data and looking at
enrichment of changes in defined "states" from Roadmap/ENCODE/whatever

 more on this later



> SampleData
>   some kind of joint sample phenodata.


this is the key, IMHO



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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