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

[Javier Pérez Florido]

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.
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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>