Entering edit mode
Jenny Drnevich
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2.2k
@jenny-drnevich-382
Last seen 10.3 years ago
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