[BioC] P calls (VSN and RMA)

[Isaac Neuhaus]

Wolfgang:

For the VSN and RMA we used only the PMvalues with the affy version 1.2.25.

raw.data <- ReadAffy(filenames=cels, sampleNames=names, verbose=F)
vsn.data <- expresso(raw.data, normalize.method="vsn", bg.correct=F, 
pmcorrect.method="pmonly", summary.method="medianpolish")
rma.data <- rma(raw.data)

Isaac


w.huber at dkfz-heidelberg.de wrote:

>Hi Petra,
>two questions:
>
>  
>
>>I used VSN data and did a filtering step ...
>>    
>>
>
>Did you use just the PM values or PM and MM (and if so, how)?
>
>  
>
>>Thus, the transition between sensitivity and selectivity occurs at
>>intensity values between 7.4 and 7.9.
>>    
>>
>
>From what other people have told me, I'd expect that there is not a
>universal value, but that it would be different for different probe
>sequences (according to the distribution of C, G, T, and A across the
>positions 1..25). Also, the exact value would depend on scanner settings
>etc. .... Opinions?
>
>Best wishes
> Wolfgang
>
>-------------------------------------
>Wolfgang Huber
>Division of Molecular Genome Analysis
>German Cancer Research Center
>Heidelberg, Germany
>Phone: +49 6221 424709
>Fax:   +49 6221 42524709
>Http:  www.dkfz.de/abt0840/whuber
>-------------------------------------
>
>  
>