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

[Chad Wayne]

I appreciate you taking the time to answer my questions.

>
> 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)
>

I loaded affy and did the search as you suggested:

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

Appears to be there along with biobase.


>> > 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.
>

I also performed the ls("package:affy") and retrieved 116 items. I  
attempted again to try the ReadAffy function and it failed.

> 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?
>

Do I need to go to terminal to change the permissions or is there a  
nice simple way to check permissions and change them accordingly if  
that is the problem. Sorry that this appears so dense, but I haven't  
quite got the hang of the unix side of OsX yet.

Thanks again,

Chad.

>  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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>           |
> | Head, Program in Computational Biology   fax:  (206) 667-1319   |
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>        |
> | Fred Hutchinson Cancer Research Center                                
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> | email: rgentlem at fhcrc.org                                             
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