[BioC] problems with sample code from "Analysis of Gene Expression Data" Chap. 4

Chris Paulse chrispaulse at hotmail.com
Thu Jul 24 16:15:24 MEST 2003


Hi,
I am running R 1.7.1 and a version of affy that I downloaded two days ago.  
I have been working through the examples in Chapter 4 from "The Analysis of 
Gene Expression Data".  First, I noticed that image display using the log 
scale as described at the bottom of p. 104 will only work for me if I change

R> image(CEL1, transfo=log())
to
R> image(CEL1, transfo=log)

That was easy, but when I move on to display plots like those in Fig. 4.5, I 
get the following:

>Data <- ReadAffy()
>boxplot(Data[,1:3],range=0)
Error in boxplot.default(data.frame(log2(intensity(x)[tmp, ])), main = main, 
  :
        formal argument "range" matched by multiple actual arguments
>mva.pairs(Data[,1:3])
Error in log(x, base) : Non-numeric argument to mathematical function

The Data Plob is valid here.  Is there any update I need to perform?

Thanks!
Chris Paulse



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