[BioC] HTqPCR and Biobase's eSet

Laurent Gautier laurent at cbs.dtu.dk
Sun Nov 27 17:11:21 CET 2011

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.



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