[BioC] Using different processed data in limma package

[Mari Miyamoto]

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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