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Question: Prokaryotic_Rhodobacter capsulatus GEP
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gravatar for James W. MacDonald
9.0 years ago by
United States
James W. MacDonald45k wrote:
Looking at the output that the OP has provided implies to me that she used the makecdfenv package to create a cdf package, but installed it incorrectly. Dorothy - you did everything correctly up until the last step. You have to use R CMD INSTALL to install any package, whether or not it has a .tar.gz suffix (which you could make using R CMD build, but this is not necessary). So just move the folder back out onto e.g., your desktop and then install. Best, Jim Martin Morgan wrote: > 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 > -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
ADD COMMENTlink modified 9.0 years ago by dorothyc130 • written 9.0 years ago by James W. MacDonald45k
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gravatar for dorothyc
9.0 years ago by
dorothyc130
dorothyc130 wrote:
Hi Jim, Thanks very much for your advice. It works now. Regards, Dorothy On Dec 1, 2008, at 5:41 AM, James W. MacDonald wrote: > Looking at the output that the OP has provided implies to me that > she used the makecdfenv package to create a cdf package, but > installed it incorrectly. > > Dorothy - you did everything correctly up until the last step. You > have to use R CMD INSTALL to install any package, whether or not it > has a .tar.gz suffix (which you could make using R CMD build, but > this is not necessary). > > So just move the folder back out onto e.g., your desktop and then > install. > > Best, > > Jim > > > Martin Morgan wrote: >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > Hildebrandt Lab > 8220D MSRB III > 1150 W. Medical Center Drive > Ann Arbor MI 48109-0646 > 734-936-8662
ADD COMMENTlink written 9.0 years ago by dorothyc130
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