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

[Ben Bolstad]

Thank you for your clear bug report, it makes tracking and fixing things
much easier. This change has been made to the development version of
affy.

Ben





On Wed, 2005-11-30 at 17:25 -0600, Jenny Drnevich wrote:
> 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
> 
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