[BioC] Agilent & LIMMA

Gordon Smyth smyth at wehi.edu.au
Fri Aug 27 02:35:13 CEST 2004

At 08:39 AM 27/08/2004, Giovanni Coppola wrote:
>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?

You can't use imageplot() with Agilent arrays processed using AgilentFE 
software, because AgilentFE does not output rows for blank/empty spots 
while limma expects to get full arrays. You can use imageplot() with 
Agilent arrays processed by Genepix or similar.

It is possible to get an image plot of Agilent/AgilentFE arrays using a 
combination of the limma and marray packages. The following code works for me:

RG <- read.maimages(fnames, source="agilent", path="AgilentFE")
y <- as(RG,"marrayRaw")
nr <- max(RG$genes$Row)
nc <- max(RG$genes$Col)
maNgr(y) <- 1
maNgc(y) <- 1
maNsr(y) <- nr
maNsc(y) <- nc
included <- rep(FALSE,nr*nc)
pos <- nc*(RG$genes$Row-1)+RG$genes$Col
included[pos] <- TRUE
maSub(y) <- included


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