[BioC] Plotting symbols for MA plot in Affycomp

James W. MacDonald jmacdon at med.umich.edu
Wed Apr 12 16:20:55 CEST 2006

Hi Monnie,

McGee, Monnie wrote:
> Dear BioC Users,
> When Affycomp gives a MA plot, there are both negative and positive
> infinities (in black ink) as plotting symbols on the plot.  I noticed
> that they are also present on the example MA plots in the Cope, et.al
> (2005) paper.  I have been unable to find an explanation of what
> these mean, and would appreciate it if someone could tell me what
> they represent. 

The Affy latin square dataset includes samples where no probe was spiked 
in (hence the concentration is 0 pMol). So the infinite fold changes 
result when the unspiked sample is in the denominator or numerator (+inf 
and -inf, respectively).

  On a related note, is placement of these positive
> and negative infinities related to the performance of the method?

I don't know about this one. Presumably there is some 'native' 
transcript for each gene (or at least some noise component for each 
probe), so the fold change shouldn't really be infinite. However, I 
don't think there is a good way to know how much transcript already 
existed in the sample to try and figure out where the infinite fold 
change points should really end up.



> Thanks, Monnie
> Monnie McGee, Ph.D. Assistant Professor Department of Statistical
> Science Southern Methodist University Ph: 214-768-2462 Fax:
> 214-768-4035
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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