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

[Javier Pérez Florido]

That's OK
Thanks Jim,
Javier


James W. MacDonald escribió:
> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives: 
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>