[BioC] limma Agilent Normalization

[Noemi Andor]

Hi,

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

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

Than I made MA plots:

plotMA3by2(Agilent.RG)	vs. 	plotMA3by2(MA )

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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