[Bioc-devel] Couple of eSet questions
sfalcon at fhcrc.org
Fri Feb 3 19:36:21 CET 2006
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
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
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
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
> 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.
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