[Bioc-devel] Couple of eSet questions

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Fri Feb 3 20:27:57 CET 2006

it sounds to me as if we are finding some use cases, and that
we want to extend eSet to cope with those that have well-defined
requirements.  all we know about assayData at present is that
it is either a list or an environment.  for twochannel data
we may want to define a specific extension of listOrEnv (i think
this is possible) that has guaranteed structure and names.
for data with standard errors we might have to do likewise.

but i would say that part of the intention of the eSet is to
require the developer always to allow an environment representation
for the assayData.  the validity criteria can impose restrictions
on this environment.

eSet itself does not need to solve the two channel or error-available
problems at once.  it should be extended to do so, with explicit
use cases stated.

Vince Carey, PhD
Assoc. Prof Med (Biostatistics)
Harvard Medical School
Channing Laboratory - ph 6175252265 fa 6177311541
181 Longwood Ave Boston MA 02115 USA
stvjc at channing.harvard.edu

On Fri, 3 Feb 2006, Seth Falcon wrote:

> 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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