[BioC] Normalizing after MAS 5.0

[Michal Blazejczyk]

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