[BioC] variable "mgu74av2cdf" was not found

[Dick Beyer]

I did a complete reinstall of R 1.6.1 and Bioconductor 1.1.  I also got mgu74av2cdf_0.1.zip from http://www.bioconductor.org/data/cdfenvs/cdfenvs.html and installed that.

Here are the main details:

> library(affy)
> library(Biobase)
> library(mgu74av2cdf)
> Data <- ReadAffy()
> eset <- rma(Data)
Error in get(x, envir, mode, inherits) : variable "mgu74av2cdf" was not found
> Data
AffyBatch object
size of arrays=640x640 features (12803 kb)
Error in get(x, envir, mode, inherits) : variable "mgu74av2cdf" was not found
Error in inherits(cdf.env, "try-error") : Object "cdf.env" not found
> 

I am using Windows 2000 and I use:

"C:\Program Files\R\rw1061\bin\Rgui.exe" --max-mem-size=768M

to start R.


In Bioconductor 1.0, things work better.  For example:
>Data <- ReadAffy()
>Data
object
CDF used=MG_U74Av2.CDF
number of chips=4
number of genes=12488
number of probe pairs=197993
annotation=
description=
notes=
size of chip=640x640
chip names=
NL_OMCATHR_H1A
NL_OWTHR_H1A
NL_YMCATHR_H1A
NL_YWTHR_H1A

I am not sure what to do next.

Thanks much,
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
*******************************************************************************