Prokaryotic_Rhodobacter capsulatus GEP
1
0
Entering edit mode
@james-w-macdonald-5106
Last seen 9 hours ago
United States
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
Epigenetics cdf affy makecdfenv plier affxparser preprocessCore Epigenetics cdf affy • 1.4k views
ADD COMMENT
0
Entering edit mode
dorothyc ▴ 140
@dorothyc-3150
Last seen 10.1 years ago
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 COMMENT

Login before adding your answer.

Traffic: 654 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6