[BioC] How do I set the median when performing MAS5.0 normalization

[James W. MacDonald]

Hi Matthew,

On 12/6/2010 11:16 AM, Matthew Willmann wrote:
> Hello,
>
> I am trying to replicate results in a published paper, where they performed a MAS5.0 normalization with the median normalized to 50 and then defined genes as present if the normalized expression value is higher than 30.  Does anyone know how I can alter the standard code to establish these parameters?
>
>> Cel.files=list.files(pattern=".CEL")
>> data.MRW=ReadAffy(filenames=Cel.files)
>> mas5(data.MRW, normalize=TRUE, sc=500)

 From the help page for mas5():

Usage:

      mas5(object, normalize = TRUE, sc = 500, analysis = "absolute", ...)

Arguments:

   object: an instance of 'AffyBatch'

normalize: logical. If 'TRUE' scale normalization is used after we
           obtain an instance of 'ExpressionSet'

So if you use mas5() with normalize = FALSE, then you don't get any 
scale normalization. You can then simply scale each chip to have a 
median of 50.

Best,

Jim


>
> Thank you for your time and advice.
>
>
> Matthew
>
>
>
> -----------------------------------------------------
> Matthew R. Willmann, Ph.D.
> Research Associate, Poethig Lab
> University of Pennsylvania
> Department of Biology
> 433 S. University Avenue
> Philadelphia, PA 19104
> Lab phone: 215-898-8916
> Cell: 508-243-2495
> Fax: 215-898-8780
>
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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.
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