[BioC] HTqPCR and Biobase's eSet

[Heidi Dvinge]

Hi Laurent & James,

thanks for the feedback on HTqPCR. Actually, I agree that 'qPCRset' really
ought to inheret from 'eSet'. It's one of these changes that I've never
gotten around to implementing, but with this gentle nudge I'll probably
implement it by the next release version. This should also facilitate
interoperability with other packages, such as what James is developing
(ReadqPCR and NormqPCR).

Best,
\Heidi

> Hi Heidi,
>
> I am currently looking iwith interest at your package HTqPCR and I have
> the following question and suggestion.
>
> The class "qPCRset" is really looking like a sort of "eSet" (defined in
> Biobase), just without "phenoData" or "assayData". Would it make sense
> to get qPCRset to inherit from "eSet" ? This would likely facilitate the
> use of functionality in "Biobase" (and free you from having to maintain
> with it).
>
> Moreover, in the documentation for the examplar datasets "qPCRraw" it is
> mentioned that the 3 TagMan arrays "are 3 different samples with 2
> replicates each". Unfortunately, the only available information
> regarding the samples are sample names such as "sample1", "sample2",
> "sample3", "sample4", "sample5", and "sample6", making it difficult to
> identify unequivocally which ones are replicates of the same sample.
> Having "phenoData" information would have made a convenient place for
> storing such information. There is indeed a supplementary file
> (mentioned in the vignette but not in the help page for the datasets
> "qPCRraw" or "qPCRpros"), where sample information are detailed but this
> is requiring to store sample information in a separate object (which was
> what the classes in Biobase were trying to help with).
>
> What do you think ?
>
> I am CC'ing the list in case someone else's would agree, or disagree.
>
>
> Best,
>
>
> Laurent
>