Hi, I'm a computational biologist at Genome Sciences Centre, Vancouver, BC, Canada. I'm working on Affymetrix custom bacterial ship, Prokaryotic_Rhodobacter capsulatus GEP. I've encountered some problems with the CDF file. I've copied the rcapex1a520469fcdf directory to /Library/Frameworks/R.framework/ Versions/2.7/Resources/library. However, I got an error as follows: -------------- > require(rcapex1a520469fcdf) Loading required package: rcapex1a520469fcdf Error in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : 'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0? > raw.data <- ReadAffy() > eset <<- rma(raw.data) Error in library("rcapex1a520469fcdf", lib.loc = NULL, character.only = TRUE) : 'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0? >library() .... plier Implements the Affymetrix PLIER algorithm preprocessCore A collection of pre-processing functions rcapex1a520469fcdf ** No title available (pre-2.0.0 install?) ** rpart Recursive Partitioning ... ------------------ Was the CDF not installed properly? I was given the cdf file, not the tar.gz file; otherwise, I'd have used R CMD INSTALL. Your feedback is very much appreciated. Thanks, Dorothy [[alternative HTML version deleted]]

Mark Robinson <mrobinson at="" wehi.edu.au=""> writes: > Hi Dorothy. > > In general you can't install packages by copying files to your library > directory. And, my guess is that your CDF *file* is not a CDF > *package*, as required by affy. Or, is it? > > Is your file a text file ... something of the this format? > http://www.affymetrix.com/support/developer/powertools/changelog /gcos-agcc/cdf.html > > If it is, you could use 'convertCdf' in the affxparser package, giving > you a CDF *file*, which you could use within aroma.affymetrix. There > also may be a way of converting this into a CDF package, but I don't > know how. Anyone else? The Bioconductor makecdfenv package makes cdf environments from cdf files. Martin > If it is not of this format, please let us know what it is. > > Mark > > > > On 28/11/2008, at 12:14 PM, dorothyc wrote: > >> Hi, >> >> I'm a computational biologist at Genome Sciences Centre, Vancouver, >> BC, Canada. I'm working on Affymetrix custom bacterial ship, >> Prokaryotic_Rhodobacter capsulatus GEP. >> >> I've encountered some problems with the CDF file. I've copied the >> rcapex1a520469fcdf directory to /Library/Frameworks/R.framework/ >> Versions/2.7/Resources/library. However, I got an error as follows: >> -------------- >>> require(rcapex1a520469fcdf) >> Loading required package: rcapex1a520469fcdf >> Error in library(package, lib.loc = lib.loc, character.only = TRUE, >> logical.return = TRUE, : >> 'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0? >> >>> raw.data <- ReadAffy() >>> eset <<- rma(raw.data) >> Error in library("rcapex1a520469fcdf", lib.loc = NULL, character.only >> = TRUE) : >> 'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0? >> >>> library() >> .... >> plier Implements the Affymetrix PLIER algorithm >> preprocessCore A collection of pre-processing functions >> rcapex1a520469fcdf ** No title available (pre-2.0.0 install?) ** >> rpart Recursive Partitioning >> ... >> ------------------ >> Was the CDF not installed properly? I was given the cdf file, not the >> tar.gz file; otherwise, I'd have used R CMD INSTALL. >> >> Your feedback is very much appreciated. >> >> Thanks, >> Dorothy >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > ------------------------------ > Mark Robinson > Epigenetics Laboratory, Garvan > Bioinformatics Division, WEHI > e: m.robinson at garvan.org.au > e: mrobinson at wehi.edu.au > p: +61 (0)3 9345 2628 > f: +61 (0)3 9347 0852 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

Hi Dorothy. In general you can't install packages by copying files to your library directory. And, my guess is that your CDF *file* is not a CDF *package*, as required by affy. Or, is it? Is your file a text file ... something of the this format? http://www.affymetrix.com/support/developer/powertools/changelog/gcos- agcc/cdf.html If it is, you could use 'convertCdf' in the affxparser package, giving you a CDF *file*, which you could use within aroma.affymetrix. There also may be a way of converting this into a CDF package, but I don't know how. Anyone else? If it is not of this format, please let us know what it is. Mark On 28/11/2008, at 12:14 PM, dorothyc wrote: > Hi, > > I'm a computational biologist at Genome Sciences Centre, Vancouver, > BC, Canada. I'm working on Affymetrix custom bacterial ship, > Prokaryotic_Rhodobacter capsulatus GEP. > > I've encountered some problems with the CDF file. I've copied the > rcapex1a520469fcdf directory to /Library/Frameworks/R.framework/ > Versions/2.7/Resources/library. However, I got an error as follows: > -------------- >> require(rcapex1a520469fcdf) > Loading required package: rcapex1a520469fcdf > Error in library(package, lib.loc = lib.loc, character.only = TRUE, > logical.return = TRUE, : > 'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0? > >> raw.data <- ReadAffy() >> eset <<- rma(raw.data) > Error in library("rcapex1a520469fcdf", lib.loc = NULL, character.only > = TRUE) : > 'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0? > >> library() > .... > plier Implements the Affymetrix PLIER algorithm > preprocessCore A collection of pre-processing functions > rcapex1a520469fcdf ** No title available (pre-2.0.0 install?) ** > rpart Recursive Partitioning > ... > ------------------ > Was the CDF not installed properly? I was given the cdf file, not the > tar.gz file; otherwise, I'd have used R CMD INSTALL. > > Your feedback is very much appreciated. > > Thanks, > Dorothy > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852