[BioC] Normalizing after MAS 5.0

[James W. MacDonald]

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
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
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