[BioC] P calls (VSN and RMA)

[Naomi Altman]

We used

norm.data <- 
expresso(raw.data,bgcorrect.method="rma",normalize.method="quantiles",
pmcorrect.method="pmonly",summary.method="mas")

I did not look at the spiking controls (I should) but the investigator did 
RT-PCR for several of the genes that expressed near 50 in all 
conditions.  A couple of these were present at low levels, but most were not.

10 seems very low to me.  After the flurry of January grants is over, I 
will have a look at the spiking controls on these arrays.

--Naomi

At 08:42 AM 1/13/2004, Isaac Neuhaus wrote:
>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
>>-------------------------------------
>>
>>
>

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
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