[BioC] Normalizing after MAS 5.0

[James W. MacDonald]

Hi Michal,

The only things in expresso() that control normalization are the 
'normalize' and 'normalize.method' arguments. If you tell expresso() to 
normalize, then your data will be normalized. If not, then you will have 
to do something additional if you want normalized data.

So it doesn't matter what you choose for PM adjustment or summary 
methods, as these have nothing to do with normalization.

Best,

Jim



Michal Blazejczyk wrote:
> Hi James,
> 
> 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?
> 
> Best regards,
> 
> Michal Blazejczyk
> FlexArray Lead Developer
> McGill University and Genome Quebec Innovation Centre
> http://genomequebec.mcgill.ca/FlexArray
> 
> 
> 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'.
> 
>> Best,
> 
>> Jim
> 
> 
> 
>> 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
>>> http://genomequebec.mcgill.ca/FlexArray
> 
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662