[BioC] Using different processed data in limma package

[Marcus Davy]

plotMA is plotting M , and A values either from an MAList object or calculated values from
an RGList using the function MA.RG to convert Red Green intensities on the raw scale
to log2 M , A values. The "array" arguement in plotMA specifies the column of the matrix of M, and A values
to be plotted.

e.g.

RG <- read.maimages(...)

MA <- normalizeWithinArrays(RG,...)
# or
MA <- MA.RG(RG)

M <- MA$M
A <- MA$A

# for array 2 data
plotMA(MA, array=2)  # spots with zero weight are not plotted by default (identified in MA$weights)
plot(A[,2],M[,2])          # all spots


marcus


>>> Mari Miyamoto <mmiyamoto_bc at yahoo.co.jp> 22/12/2004 1:22:30 AM >>>
Hello again,

I could manage to give the color for the MA plot using
ProcessedSignal. 

If possible I still want to know how to obtain those
values used in plotMA.

Thanks!
Mari


--- Mari Miyamoto <mmiyamoto_bc at yahoo.co.jp> 
Hi all,
> 
> I've been using limma with Agilent data.
> By following the user guide, I could make MA plot
> with
> color based on information of the Spot Types File
> (STF). 
> 
> I'd like to import data which use different data
> processing and give them color using the STF.
> When I import those value just using read.table, I
> miss
> the STF information and can
> 't give the color to the MA plot. 
> 
> If I can convert value of M and A those are used in
> plotMA
> in limma, I will be able to replace them but I don't
> know
> how to obtain M and A value which are used for
> plotMA.
> 
> If I can use rProcessedSignal and gProcessedSignal
> which
> are originally in the output of the Feature
> Extraction
> software, that would be fine. 
> 
> If anyone has any idea, that would be great helpful.
> 
> Thank you.
> 
> Mari
> 
> 
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