variable "mgu74av2cdf" was not found
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Dick Beyer ★ 1.4k
@dick-beyer-26
Last seen 10.3 years ago
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 ********************************************************************** *********
cdf probe cdf probe • 1.2k views
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Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 10.3 years ago
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
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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 > > >
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On 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. I have uploaded new CDF data packages to the website for Win32. As near as I can tell, they correct this problem, although if someone can confirm this, it would be much appreciated. -J
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