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Jiuzhou song ▴ 100
@jiuzhou-song-1051
Last seen 9.6 years ago
Hi, Fellows: I want to install bioconductor on Sun, machine hardware sun4u, version 5.9 operator system, sparc processor. After I loaded affy, I met some issues: >library(affy) Loading required package: tkWidgets Loading required package: widgetTools Loading required package: tcltk Error in firstlib(which.lib.loc, package) : Tcl/Tk support is not available on this system Error: package 'tcltk' could not be loaded >list.celfiles() Error: couldn't find function "list.celfiles" It seems all commends from affy can not work here. Why? any help from you would be greatly appriated. Thanks. John
affy affy • 777 views
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 9.6 years ago
Hi John, The output you sent indicates that the tcltk package is required for use of affy. For the tcltk R package to work, you have to install Tcl/Tk libraries on the system. Try installing Tcl/Tk and then trying again. + seth On Wed, Jan 12, 2005 at 02:19:01PM -0700, Jiuzhou song wrote: > Hi, Fellows: > I want to install bioconductor on Sun, machine hardware sun4u, version 5.9 > operator system, sparc processor. After I loaded affy, I met some issues: > >library(affy) > Loading required package: tkWidgets > Loading required package: widgetTools > Loading required package: tcltk > Error in firstlib(which.lib.loc, package) : > Tcl/Tk support is not available on this system > Error: package 'tcltk' could not be loaded > >list.celfiles() > Error: couldn't find function "list.celfiles"
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@maria-ines-zanor-1076
Last seen 9.6 years ago
I would like to ask whether there is a cdf file available for the Arabidopsis 8K Affymetrix chip (the first one). I would like to normalize data with RMA software. Thank you in advance MInes
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Mines, I'm not familiar with the arabidopsis chips, but you did check (http://www.bioconductor.org/data/metaData.html) and didn't find it? Sean On Jan 17, 2005, at 12:33 PM, Maria Ines Zanor wrote: > I would like to ask whether there is a cdf file available for the > Arabidopsis 8K Affymetrix chip (the first one). I would like to > normalize data with RMA software. > Thank you in advance > > MInes > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor
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Sean Davis wrote: > Mines, > > I'm not familiar with the arabidopsis chips, but you did check > (http://www.bioconductor.org/data/metaData.html) and didn't find it? She shouldn't even need to check. The affy package has automagic download of necessary cdfenvs, so all that is needed is something like: abatch <- ReadAffy() abatch If the cdfenv isn't available, it will error out. Otherwise the correct one will be downloaded and installed for you. Jim > > Sean > > On Jan 17, 2005, at 12:33 PM, Maria Ines Zanor wrote: > >> I would like to ask whether there is a cdf file available for the >> Arabidopsis 8K Affymetrix chip (the first one). I would like to >> normalize data with RMA software. >> Thank you in advance >> >> MInes >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109
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