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

[Matthew Willmann]

Hi Jim,

Thank you.  Does this mean that I can obtain the desired normalization by the following?

mas5(data.MRW, normalize=FALSE, sc=50)


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

On Dec 6, 2010, at 3:55 PM, James W. MacDonald wrote:

> 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
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