[BioC] Using different processed data in limma package

[Giovanni Coppola]

Hi Marcus and Mari,
ok, but how to create MAList objects starting by Agilent normalized data?
In other words, is it possible to bypass the normalization step and to 
apply fit and EBayes to green and red processed signals from the Agilent 
output?
This is to compare the top genes identified a) starting by the Agilent 
normalized data and 2) following the limma pipeline
It would be nice to have kind of MAa<-MA.Ag(Agilent dataset) command, 
reading the rProcessedSignal and gProcessedSignal columns from the Agilent 
dataset and creating the MAList object to be analyzed with fit and EBayes
Any suggestions?
Thanks
Giovanni


At 05:47 PM 12/21/2004, you wrote:

>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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