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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