[BioC] Using different processed data in limma package

[Mari Miyamoto]

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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