Dear list,
 
I am using an ExpressionSet and generating figures using subsets of genes via boxplot (oligo) and plotlines (limma).
 
> class(zf.rma.sub1)
[1] "ExpressionSet"
attr(,"package")
[1] "Biobase"

My data in the expression set is log2-transformed, as expected:
 
> exprs(zf.rma)[1:3,1:2]
         220302_4-24-08_1cell_0004_532.xys 220302_4-24-08_1cell_0004_635.xys
AA494792                         14.730366                         14.623973
AA494800                         14.314152                         13.728564
AA494831                          6.960698                          6.748818

My lineplots also look fine, but for some reason the y-axis on my boxplots automatically converts to log10 and I can only fix it by doing something stupid and clunky like this after I call the boxplot:
 
axis(2, at=c(3.0,3.2,3.4,3.6,3.8,4.0),  lab=c("6","8","10","12","14","16"))
 
which isn't actually precise anway. Any ideas?
 
Many thanks,
 
Farhad Imam
  
-------------------------------------------------- 
Farhad Imam, MD, PhD 
Postdoctoral Fellow, Schier Lab 
Department of Molecular and Cellular Biology 
Harvard University 

(617) 496-4910 
fimam@mcb.harvard.edu

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