[BioC] can't get CDF variable

[Dick Beyer]

Hi Rafael,

Actually, it is a little more obscure.  I rolled back to affy_1.0.9.zip, and I did not get the error message.  So I suppose something broke between affy_1.0.9.zip and affy_1.1.zip.

Thanks,
Dick

*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Environmental Health, Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
			Seattle, WA 98105-6099
*******************************************************************************








On Tue, 19 Nov 2002, Rafael A. Irizarry wrote:

> in version 1.1, except for hgu95av2 and hgu133a chips, you must 
> download probe location infromation in the form of a package.
> 
> downlaod  and install the package
> 
> mgu74av2cdf
> 
> from
> 
> http://www.bioconductor.org/data/cdfenvs/cdfenvs.html
> 
> notice there is a "whats different" section 
> in the vignette 
> 
> hope this helps,
> rafael
> 
> On Tue, 19 
> Nov 2002, 
> Dick Beyer wrote:
> 
> > I get an error when running rma: variable "mgu74av2cdf" was not found.  I have loaded the relevant package.  Here are more details:
> > 
> > R : Copyright 2002, The R Development Core Team
> > Version 1.6.1  (2002-11-01)
> > > library(affy)
> > Welcome to Bioconductor 
> >          To view some introductory material -- look at our vignettes
> >          Simply type: openVignette() 
> >          to see the available vignettes
> >          To read a vignette see the openVignette help page for details
> > Creating a new generic function for "summary" in package Biobase 
> > 
> > Attaching package `Biobase':
> > 
> > 
> >         The following object(s) are masked from package:base :
> > 
> >          split summary 
> > 
> > 
> > Attaching package `affy':
> > 
> > 
> >         The following object(s) are masked from package:base :
> > 
> >          barplot boxplot colnames hist history image ncol nrow 
> > 
> > > library(mgu74av2cdf)
> > > Data <- ReadAffy()
> > > eset <- rma(Data)
> > Error in get(x, envir, mode, inherits) : variable "mgu74av2cdf" was not found
> > > 
> > 
> > Not sure what to do next.
> > 
> > Thanks,
> > Dick
> > *******************************************************************************
> > Richard P. Beyer, Ph.D.	University of Washington
> > Tel.:(206) 616 7378	Environmental Health, Box 354695
> > Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
> > 			Seattle, WA 98105-6099
> > *******************************************************************************
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
>