On Sat, Jun 19, 2010 at 1:27 AM, Noemi Andor <Noemi.Andor@campus.lmu.de>wrote:

> Hi,
>
> I'm working with the Agilent CGH 244A Platform, and I normalized the data
> using the command:
>

MA <- normalizeWithinArrays(Agilent.RG, method="loess")
>
>
Hi, Noemi.

You do not want to be normalizing CGH arrays using loess normalization, I do
not think.


> Than I made MA plots:
>
> plotMA3by2(Agilent.RG)  vs.     plotMA3by2(MA )
>
>
Best to include the exact code that you are using and the output of
sessionInfo().


> Yet I get the same plots, i.e. normalization had no effect upon the data
> (see attached plots).
> I read something about weightening particular spots within the
> normalization, would that be a solution, considering the attached plots?
>
> I would also like to have a fitting curve in each plot. I read the command:
>
> plotPrintTipLoess(RG)
>
> would create such plot, but here I get the error that some layout object is
> missing (ngrid.r, ngrid.c - number of grid rows/columns on the arrays - do
> not know where to extract that information)
>
> Or is there any other solution to do this?
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