[BioC] Normalizing after MAS 5.0
michal.blazejczyk at mail.mcgill.ca
Wed Jan 21 23:25:06 CET 2009
What I was wandering about more specifically was: if I run expresso
with a different summary.method parameter (say, medianpolish for RMA),
but select mas as the PM correction method or the background correction
method, should I be worrying about the additional normalization as well?
Or is it only applicable if I use summary.method=mas regardless of my
pmcorrect.method and bgcorrect.method?
FlexArray Lead Developer
McGill University and Genome Quebec Innovation Centre
James W. MacDonald <jmacdon at med.umich.edu> wrote:
> Hi Michal,
> Technically, the mas5 method is implemented by the function mas5(),
> so you would certainly need to normalize after that step. Note that
> mas5() is just a wrapper to expresso:
> res <- expresso(object, bgcorrect.method = "mas", pmcorrect.method =
> "mas", normalize = FALSE, summary.method = "mas", ...)
> As for expresso(), this is a bit of a 'roll your own' function, so
> it is incumbent upon the user to figure out whether or not the data
> need to be normalized, which would be dependent on the arguments
> 'normalize' and 'normalize.method'.
> Michal Blazejczyk wrote:
>> Hello group,
>> According to the Bioconductor Help for function expresso():
>> "For the mas 5.0 and 4.0 methods ones need to normalize after
>> obtaining expression. The function affy.scalevalue.exprSet
>> does this."
>> What does it really mean, "for the mas 5.0 method" in this case?
>> When calling expresso, "mas" can be set as a method for background
>> correction, PM correction, and probe summarization. In which of
>> these cases should the custom normalization (affy.scalevalue.exprSet)
>> be used?
>> Best regards,
>> Michal Blazejczyk
>> FlexArray Lead Developer
>> McGill University and Genome Quebec Innovation Centre
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