[BioC] Agilent & LIMMA

[Giovanni Coppola]

Dear all,
I am analizyng Agilent G4121A mouse chips with LIMMA.
My first three problems:
1) Layout: from the GAL file provided with the chip (and from the flat
output file), I can only obtain the rows (105), and the columns (215). No
information about the layout... is this due to the different technology
(without printing tips)? If this is the case, I guess I don't need the
printtiploess normalization. Is that correct? But what about the imageplot?
How should I set the layout parameters in this function?

2) Is there a way (I am sure there is) to use the spot type information
(stored in RG$genes$Status) also after the lmFit analysis (i.e. in the qqt
plot and in the plot(A,M,pch=16,cex=0.1))? I would like to have the same
colors for control spots also in these plots.

3) about the internal controls and duplicate spots on the Agilent arrays,
their meaning is not clearly exposed in the accompanying documentation. I
emailed the technical support, and they said that this information was
developed with Rosetta (their analysis software), so it is not available to
their customers... Don't you think this is a limitation of the analysis? Do
you have more information about this?

Thank you for your help
** hoping I did not post too much RTFM questions :-] **

Giovanni