[BioC] double-logging in MAplot(abatch, pairs=T)

Jenny Drnevich drnevich at uiuc.edu
Thu Dec 1 00:25:50 CET 2005


I would like to suggest a change to the code for MAplot. When you call 
MAplot(pairs=TRUE) for Affybatch objects, double logs are taken; you can 
see this in the affy vignette (Oct 13, 2005) on pg 11 - the A values only 
range from 2 - 4. MAplot by default takes the logs, but so does mva.pairs, 
which is called when pairs=T. One solution is to use MAplot(abatch, 
pairs=T, log=F) , but it would easier if the MAplot code for Affybatch 
objects was changed to:

if (!pairs) { lots of stuff omitted }
else {
             if (is.null(subset))
                 subset <- 1:ncol(x)
             mva.pairs(x[, subset], log.it=FALSE...)    ##add the log.it=F 

Maybe this is what Simon Lin was having trouble with in his Nov 14, 2005 


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

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

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