[BioC] Affy 1.5.8 functions not working on Mac OS X 10.3

[Robert Gentleman]

On Jan 24, 2005, at 12:55 PM, Chad Wayne wrote:

> It was recommended that I post this problem to the mailing list. I am  
> unable to get affy to work, e.g. the library loads into R, but the  
> functions don't seem to work. I was hoping someone may have seen this  
> problem before and may have a solution. I am working in the correct  
> working directory.
>
> I am using version v2.0.1 of R with the default Bioconductor package  
> installed. Current package of Affy is 1.5.8. I am using Mac OS X  
> 10.3.7 and running X11 (X11 1.0 - XFree86 4.3.0). This is a shared  
> environment and all packages were installed in the top library, not in  
> the User library.
>
> On prompt:
> > load("/nnn/nnn/nnn/timecourse.RData")

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

So, if you go
   search()
at this point you should get something like:
 > search()
  [1] ".GlobalEnv"         "package:affy"       "package:reposTools"
  [4] "package:Biobase"    "package:tools"      "package:methods"
  [7] "package:stats"      "package:graphics"   "package:grDevices"
[10] "package:utils"      "package:datasets"   "Autoloads"
[13] "package:base"

The important things are for affy and Biobase to be there (at least  
given what you are saying below)

> > ReadAffy(widget=T)
> Error: couldn't find function "ReadAffy"
> > ReadAffy()
> Error: couldn't find function "ReadAffy"
> > pData(eset)
> Error: couldn't find function "pData"
>


You can also try something like
ls("package:affy")

which should show about 116 things (mostly functions) and one should be  
ReadAffy.

If not, then the installation is not correct. Are you sure they have  
global read permission etc on the R library directory and all contents?  
Have you checked to see if there are any files
in those directories?

  Robert

> I've also attempted to "start from scratch" from the original .cel  
> files and get the same type of error message that the function  
> couldn't be found.
>
> I have checked to ensure that affy is installed and loaded, and based  
> on the Package Manager, it is .
>
>
> I've also tried using limma (v1.8.10), and had no problems, other than  
> I can't read in the eset.
>
> > packageDescription("limma", field="Version")
> [1] "1.8.10"
> > packageDescription("affy", field="Version")
> [1] "1.5.8"
> > version
>          _
> platform powerpc-apple-darwin6.8
> arch     powerpc
> os       darwin6.8
> system   powerpc, darwin6.8
> status
> major    2
> minor    0.1
> year     2004
> month    11
> day      15
> language R
>
>
> Thanks for the assistance.
>
> Chad Wayne
>
> Chad M. Wayne, Ph. D.
> Baylor College of Medicine
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
>
>
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| Robert Gentleman              phone: (206) 667-7700                    
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| Head, Program in Computational Biology   fax:  (206) 667-1319   |
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