[Bioc-devel] Couple of eSet questions

Seth Falcon sfalcon at fhcrc.org
Fri Feb 3 20:12:21 CET 2006

On  3 Feb 2006, sdavis2 at mail.nih.gov wrote:
>> 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 was making up the specifics and it shows ;-)
Where I think we agree, is that technology specific data structures
might be best represented as part of the class structure not left to
an ad-hoc how to use list names setup.

> 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 differently.

Right, this was supposed to be not-analogous apart from wanting to
have a single place to put the metadata.  

+ seth

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