[Bioc-devel] Couple of eSet questions

Sean Davis sdavis2 at mail.nih.gov
Fri Feb 3 20:02:20 CET 2006

On 2/3/06 1:36 PM, "Seth Falcon" <sfalcon at fhcrc.org> wrote:

> More thoughts on eSet...
> On  2 Feb 2006, sdavis2 at mail.nih.gov wrote:
>> Since we are talking about eSets, I thought I would ask a couple
>> more questions.
>> 1)  What is the thinking as to "standard use" for two-color data and
>>     eSets?
> That's a good question.  For me it points to a downside of the notion
> of an "everything set".  In its currnet form, "standard use" for
> two-color data would require a convention for how to name the
> assayData elements.
> I think the notion of grouping together assay data that shares
> reporterInfo and phenoData is a good one, but I wonder if the actual
> data storage/access is best handled by technology specific subclasses.
> Here are three usage scenarios:
> 1. Two-color data.  Want to store two expression matrices for red and
>    green scans along with an associated standard error matrix for
>    each.  

What about a "channel" data structure which would include the label used
(Cy3, Cy5, etc.), of which there can be 1..2?

I still think there needs to be an accepted data matrix and associated error
matrix for the whole dataset, though.  This would represent the normalized
and processed data to be used in any further analysis.

> 2. Time-course data.  Same samples, same chip.  Want to store
>    timepoint expression matrix pairs.

Time course data needs to be combined with metadata in order to be useful.
I'm not sure that two-color data and time-course data are analogous from
that point of view, but I may just be thinking about it slightly


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