[BioC] Bioconductor Digest, Vol 45, Issue 9

[Dick Beyer]

Please ignore my previous submission.  As Martin Morgan kindly pointed out to 
me, I was using an old version of simpleaffy.  Updating to 2.8.0 eliminated my 
problem.

Thanks,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
 			Seattle, WA 98105-6099
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
http://staff.washington.edu/~dbeyer
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> ------------------------------
> 
> Message: 9
> Date: Wed, 8 Nov 2006 14:15:59 -0800 (PST)
> From: Dick Beyer <dbeyer at u.washington.edu>
> Subject: [BioC] simpleaffy gives error: unable to find an inherited
> 	method for function "pData"
> To: Bioconductor <bioconductor at stat.math.ethz.ch>
> Message-ID:
> 	<Pine.LNX.4.43.0611081415590.12784 at hymn08.u.washington.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
> 
> I've run into an error using simpleaffy on linux.  I am running R in a 
> directory that contains several CEL files.
> 
> library(simpleaffy)
>> affyRaw <- ReadAffy()
> Error in function (classes, fdef, mtable)  :
>         unable to find an inherited method for function "pData", for 
> signature "phenoData"
> 
>> sessionInfo()
> R version 2.4.0 (2006-10-03)
> x86_64-unknown-linux-gnu
> 
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
> [7] "datasets"  "base"
> 
> other attached packages:
> simpleaffy       affy     affyio    Biobase
>    "2.2.0"   "1.12.0"    "1.0.0"   "1.12.2"
> 
> If I redo this without simpleaffy, then all is well.
> 
> Thanks,
> Dick
> *******************************************************************************
> Richard P. Beyer, Ph.D.	University of Washington
> Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
> Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
> 			Seattle, WA 98105-6099
> http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html
> http://staff.washington.edu/~dbeyer
>