[Bioc-devel] Couple of eSet questions

[Seth Falcon]

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.  

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

3. Combine 1 & 2.

While I can imagine ways to use eSet for all three, they would all require
ad-hoc naming schemes for the elements of the assayData slot.  Here,
there may be a real advantage to a technology-specific subclass that
defines an appropriate structure (redExprs, greenExprs, etc).

Another angle is to search for methods that make sense across
different technologies:

  description()
  notes()
  annotation()
  history()?
  phenoData()
  reporterInfo()
  sampleNames()
  reporternames()

>
> 2)  With regard to reporterInfo, is there going to be a constraint
>     to keep
> the single-column data.frame idea as presented in the vignette, or is that
> slot meant to be more flexible (left as a generic data.frame)?

Seems to me that reporterInfo and phenoData slots should contain the
same class, a data.frame with some additional meta data.

+ seth