[BioC] Agilent & LIMMA

[Gordon Smyth]

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)?

Yes it is. Agilent doesn't have print tips.

>  If this is the case, I guess I don't need the
>printtiploess normalization. Is that correct?

I recommend method="loess".

>  But what about the imageplot?
>How should I set the layout parameters in this function?

Set ngrid.c=1, ngrid.r=1. BTW this will cause method="printtiploess" and 
method="loess" to be the same at the normalization step.

>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.

You can pass an argument col to qqt() or to plot(). This is a vector of 
integers or colour names ("red", "green" etc) of the same length as the 
number of points. E.g.,

plotcol <- RG$genes$Status
plotcol[RG$genes$Status=="Control"] <- "red"
plotcol[RG$genes$Status=="Gene"] <- "black"
qqt(fit$t, col=plotcol)

>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?

We haven't been able to get further information on the controls from 
Agilent either. It would certainly be nice to know they are but it doesn't 
limit the analysis. Many other arrays don't have these controls in the 
first place.

Gordon

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