[BioC] default BG subtraction in plotMA...

[Marcus Davy]

Hi,
Default function arguements in limma use background subtraction of
information (Section 6.1 p20, 20-Apr-2006 edition). I guess more clarity
could go into the help pages for plotMA and plotMa3by2 themselves ( This
applies to plotPrintTipLoess aswell).

A simple way to change the behaviour is to remove the Rb, and Gb components
of the "RGList" so background subtraction cannot be done, you can do this
manually or use functions as your've already illustrated which essentially
do this for you. e.g.

#Background subtraction
plotMA(RG)
plot(backgroundSubtract(RG, method="subtract")

# No background subtraction
plot(backgroundSubtract(RG, method="none")



Marcus


On 5/10/06 2:58 AM, "Jenny Drnevich" <drnevich at uiuc.edu> wrote:

> 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
> 
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