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

[Jenny Drnevich]

Hi,

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 
option
         }
     }

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

Cheers,
Jenny


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