[BioC] HTqPCR and Biobase's eSet
laurent at cbs.dtu.dk
Sun Nov 27 17:11:21 CET 2011
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
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.
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