[BioC] default BG subtraction in plotMA...

[Jenny Drnevich]

Hi Gordon,

I ran across this non-documentation a while back when trying to visualize 
my raw data, and now after having to point it out to three separate people 
I realized I should tell you about it. When you pass an RGList to 'plotMA' 
or 'plotMA3by2' it gets converted to a MAList by 'MA.RG', which by default 
will do a simple background subtraction if there are $Rb and $Gb items in 
the RGList. However, it's not documented anywhere in 'plotMA' or 
'plotMA3by2' that the plots will be of background-subtracted values if 
background correction has not been done, nor is there anyway to change this 
behavior within the calls. The other people and myself thought we were 
looking at raw, non-background corrected data and didn't realize that many 
spots were removed because of non-positive values after background 
subtraction. At the very least, would you add a sentence to the help files 
mentioning that background subtraction will be done by default? Being able 
to change the background correction in the call to 'plotMA' or 'plotMA3by2' 
would be nice, but as I've told people, you can do it yourself with one 
extra command:

MA <- MA.RG(RG, bc.method="none")
plotMA(MA)

Thanks,
Jenny

BTW - I apologize if this has already been changed since limma 2.4.7 - I'm 
in the middle of several analyses and haven't wanted to upgrade to R 2.3.0 yet.



Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
fax: 217-265-5066
e-mail: drnevich at uiuc.edu