[BioC] getting normexp (and log2 transformed) values - not further-processed M values

[adoty at umd.edu]

Dear Dr. Smyth,

Thanks so much for your quick and helpful reply.  Yes, I think you are right to say "just use R!"  I never had before I began to analyze my RIP-CHiP data set (hence the non-standard use of limmaGUI) - but I have indeed thoroughly read the limma user's manual (and I also tried general R help documentation and the limma "user manual" to investigate R more...)

Anyway, your help allowed me to solve a similar "output" problem in another R package (eCADS).  I also see that by using the "exprs.MA(MA)" statement, I can recover normalized, log2 transformed individual values for both the red and green channels for all my arrays.

Thank you very much again for your help.

Sincerely,
Alana

 
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From: Gordon K Smyth <smyth at wehi.EDU.AU>
Subject: [BioC] getting normexp (and log2 transformed) values - not
	further-processed M values
Date: Wed, 7 Oct 2009 09:25:42 +1100 (AUS Eastern Daylight Time)
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