[BioC] Arguments for normalizewithinarrays (Limma)

[J.delasHeras at ed.ac.uk]

Quoting Sally <sagoldes at shaw.ca>:

> I am trying to understand what values I should put in for the   
> following arguments.  For example how many iterations should I use.   
>  What is a good value for span, df etc.?  Can anyone guide me?  Is   
> there a good reference source for this information?
>
> normalizeWithinArrays(object, layout, method="printtiploess",   
> weights=object$weights, span=0.3, iterations=4, controlspots=NULL,   
> df=5, robust="M", bc.method="subtract", offset=0)
>
> 	[[alternative HTML version deleted]]

I found the function 'scatter.smooth' very useful for this. It will  
plot a scatterplot (from a given set of data) and display the loess  
curve fit according to a number of parameters. That allows you to see  
how the fit changes as you change the number of iterations, and the  
span, etc.

check ?scatter.smooth

The defaults in Limma ('normalizeWithinArrays')are generally more than  
adequate, 'though.

Jose


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Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
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