[BioC] pseudo median reference

[James W. MacDonald]

Hi Sundar,

sundar Venkat wrote:
> Dear Users,
>                  MAplot(affy) (ma.plot function), by default considers the pseudo-median reference chip.
> I would like to know how it is calculated ? if at probe level or probe set level what does the pseudo median reference signify.

The MAplot() function takes an AffyBatch as input, so by definition the 
plot is at the probe level. It is calculated by extracting the probe 
data and running the rowMedians() function, which will give you a median 
value for each probe.

If you want to peruse the function yourself, you can do so by

showMethods("MAplot", includeDefs = TRUE)

Best,

Jim


>  
> can any one suggest some reference on this.
> 
> thank you ,
> Sundar
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
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1241 E. Catherine St.
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