[BioC] variable "mgu74av2cdf" was not found

Rafael A. Irizarry rafa@jhu.edu
Wed, 20 Nov 2002 14:31:42 -0500 (EST)


no they have not. right now i have no way of doing it. ill ask the gurus.
-rafael

On Wed, 20 Nov 2002, Ben Bolstad wrote:

> I can duplicate your errors on a fresh windows 2000 installation of R
> 1.6.1 and bioconductor (getBioC), both using mgu74av2cdf and hgu95acdf 
> data. 
> 
> No such problem trying the equivalent on a linux machine. 
> 
> On a linux machine
> 
> > library(mgu74av2cdf)
> > mgu74av2cdf
> <environment: 0x8b3a8b0>
> 
> On a windows machine
> 
> > library(mgu74av2cdf)
> > mgu74av2cdf
> Error: object "mgu74av2cdf" not found
> 
> Rafael: have the cdfenvs been tested on win? digging around in the
> installed cdfenvs on win i can't find the equivalent to the .First.lib,
> does not appear that the datafiles are being attached properly on win.
> 
> Thanks,
> 
> Ben
> 
> 
> > 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
> > *******************************************************************************
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> 
>