[BioC] problems with affy function indexProbes on Mac

[drnevich at uiuc.edu]

Hi all,

I'm working with a friend who just installed R and Bioconductor yesterday using the precompiled Max OSX binaries and biocLite. We're having some problems with indexProbes, and I can't see an obvious reason why. Archives weren't helpful.


> library(affy)
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

    Vignettes contain introductory material. To view, type
    'openVignette()' or start with 'help(Biobase)'. For details
    on reading vignettes, see the openVignette help page.

Loading required package: affyio
> rawdata <- ReadAffy()

> library(made4)
Loading required package: ade4
Loading required package: scatterplot3d
> overview(rawdata)
Error in function (classes, fdef, mtable)  : 
	unable to find an inherited method for function "indexProbes", for signature "AffyBatch", "list"

> temp <- indexProbes(rawdata)
Error in function (classes, fdef, mtable)  : 
	unable to find an inherited method for function "indexProbes", for signature "AffyBatch", "missing"
> sessionInfo()
R version 2.4.0 (2006-10-03) 
powerpc-apple-darwin8.7.0 

locale:
en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] "tools"     "methods"   "stats"     "graphics"  "grDevices"
[6] "utils"     "datasets"  "base"     

other attached packages:
        made4 scatterplot3d          ade4          affy        affyio 
      "1.8.0"      "0.3-24"       "1.4-2"      "1.12.1"       "1.2.0" 
      Biobase 
     "1.12.2" 

Is this a bug?

Thanks,
Jenny
Jenny Drnevich, Ph.D.
Functional Genomics Bioinformatics Specialist
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801

ph: 217-244-7355
fax: 217-265-5066 
e-mail: drnevich at uiuc.edu