[BioC] Re-scaling MA plot Y axis in LimmaGUI?

J.delasHeras@ed.ac.uk J.delasHeras at ed.ac.uk
Thu Dec 1 18:41:19 CET 2005

Quoting Keith Satterley <keith at wehi.edu.au>:

> If an M value is not being plotted, try a different background
> correction method. The Subtract method(the default in limmaGUI) may
> produce some negative values, which are hence excluded. Use None

I forgot to add to this that this doesn't seem to be the problem. At 
first I thought of this possibility, as that particular gene shows no 
signal above background in one channel (it's a gene that is normally 
silent but I can activate after a treatment)... but even using no 
background substraction doesn't bring it into view. It surprises me, as 
it does appear in the toptable, first of the list, in fact, so I guess 
Limma doesn't just remove it...

yours sincerely puzzled,


Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131 6513374
Institute for Cell & Molecular Biology        Fax:   +44 (0)131 6507360
Swann Building, Mayfield Road
University of Edinburgh
Edinburgh EH9 3JR

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