Greetings,
I'm kicking tires on the new DESeq2 package -- very nicely done, btw,
thanks!.
I have a quick question about the use of the variance and rlog
transformations.
It seems that both functions prefer to receive a DESeqDataSet with a design
set to formula(~ 1). I say "prefer" because while rlogTransformation will
error-out when the incoming dds has a different formula, the
varianceStablizingTransform walks through it.
If this in fact is the case, would it make sense to simply ensure this to
be true by specifically hammering the design() of the dds to be as such
from within the function itself?
Unless I am missing something (if so, feel free to point it out), it seems
like it would make the end-user's life easier w/o sacrificing much
(anything) as the user wouldn't be forced to make a copy of the dds to pass
to the function before it is called (and perhaps firing off a warning()
when the incoming dds need to be changed as such).
Thanks again,
-steve
--
Steve Lianoglou
Computational Biologist
Department of Bioinformatics and Computational Biology
Genentech
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