[BioC] How to do normalization without background subtraction in limmaGUI or limma?

James Wettenhall wettenhall at wehi.edu.au
Mon Oct 20 07:22:02 MEST 2003

> >I just wonder is there any option to do normalization in limmaGUI or limma
> >WITHOUT background subtraction?
> RG <- backgroundCorrect(RG,method="none")
> MA <- normalizeWithinArrays(RG)
> Note: you need a more recent version of limma than the BioC release 1.2.
> Gordon

Avoiding background subtraction in this way is not yet possible
in limmaGUI via widgets, but you can always edit copies of your 
image analysis files (Spot or GenePix or ...) to include columns 
of zeroes for the background.  

Soon I will be adding some documentation to limmaGUI, to make it 
easier to fiddle with the internal limma objects via the 
"Evaluate R Code" window.
You can do
RG <- backgroundCorrect(RG,method="none")

But then any existing MA objects will be out of date, so it's 
best to start a new analysis, then run the backgroundCorrect 
command above, then check the value of MA.Available via the 
Evaluate R Code window will show you that the only MA object 
which has been automatically created is MAraw 
(unnormalized), (not MAwithinArrays, MAbetweenArrays or MAboth), 
so you should overwrite this with 
MAraw <- MA.RG(RG)
after using background correct "none" to overwrite the default 

Unless you've been doing some serious "hacking" :) the values 
in the MA.Available list object seen in the "Evaluate R 
Code" window should be consistent with those in the drill-down 
status widget.


James Wettenhall                                  Tel: (+61 3) 9345 2629
Division of Genetics and Bioinformatics           Fax: (+61 3) 9347 0852
The Walter & Eliza Hall Institute         E-mail: wettenhall at wehi.edu.au
 of Medical Research,                     Mobile: (+61 / 0 ) 438 527 921    
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