[BioC] running MBEI (PM-MM) using expresso

[James W. MacDonald]

Hi Javier,

Javier Pérez Florido wrote:
> Thanks Jim, but, what is the method to be used in the background 
> correction? I have read that in this step (background) the MM 
> intensities are substracted.

This is just a question of semantics. What you want is for the MBEI 
method to be fit on the PM-MM data - does it really matter if you say 
"I'm going to subtract MM from PM as a background correction." or if you 
say "I'm going to subtract MM from PM as a PM correction method."?

In the end you have done the same thing.

Best,

Jim


> Thanks again,
> Javier
> 
> 
> James W. MacDonald escribió:
>> Hi Javier,
>>
>> Javier Pérez Florido wrote:
>>> Hi all,
>>>
>>> The MBEI method has two versions: PM-only and PM-MM.
>>> PM-only model performs no background correction, Invariant Set for 
>>> normalization, PM only for PM correction and the Multiplicative Model 
>>> for summarization. Using expresso:
>>> eset<-expresso(affyBatch,bgcorrect.method="none",normalize.method="invariantset", 
>>> pmcorrect.method="pmonly",summary.method="liwong")
>>>
>>> But, what is the expresso command for the PM-MM model?
>>
>> pmcorrect.method = "subtractmm"
>>
>> > pmcorrect.methods()
>> [1] "mas"            "methods"        "pmonly"         "subtractmm"
>> [5] "orrect.methods"
>>
>>
>> Best,
>>
>> Jim
>>
>>
>>>
>>> Thanks in advance,
>>> Javier
>>>
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>>
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826