[BioC] ReadAffy question

[James W. MacDonald]

Hi Loren,

Loren Engrav wrote:
> I have R and Bioconductor and X11 and tkWidgets and widgetTools working on
> Mac OS 10.4.8

We need more information than that. What is the ouput from sessionInfo()?

> 
> I enter
> 
>>library(affy)
> 
> 
> And then
> 
>>mydata <- ReadAffy(widget=TRUE)
> 
> 
> And then get
> 
> Error in new.env(hash = TRUE, parent = NULL) :
>     use of NULL environment is defunct
> Error in function (classes, fdef, mtable)  :
>     unable to find an inherited method for function "pData", for signature
> "NULL"
> 
> Whereas if I enter
> 
>>mydata <- ReadAffy()
> 
> 
> All goes well
> 
> How do I fix this?

I wonder if you have a newer version of R with an old version of affy or 
Biobase. I am not on a Mac, so I can't test. However, it works for me on 
windows:

 > dat <- ReadAffy(widget=T)
Loading required package: tkWidgets
Loading required package: widgetTools
Loading required package: tcltk
Loading Tcl/Tk interface ... done
Loading required package: DynDoc
 > sessionInfo()
R version 2.4.1 (2006-12-18)
i386-pc-mingw32

locale:
LC_COLLATE=English_United States.1252;LC_CTYPE=English_United 
States.1252;LC_MONETARY=English_United 
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
   tkWidgets      DynDoc widgetTools        affy      affyio     Biobase
    "1.12.1"    "1.12.0"    "1.10.0"    "1.12.2"     "1.2.0"    "1.12.2"

Best,

Jim


> 
> Thank you
> 
> 
> ---from
> 
> ...all creatures great and small...
> 
> Loren H. Engrav, MD
> Professor, Division of Plastic Surgery
> Harborview Med Ctr, 359796
> 325 Ninth Avenue
> Seattle, WA 98104
> office 206 731 3209
> fax 206 731 3656
> email engrav at u.washington.edu
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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