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Hi Claire, claire wrote: > Hello there, > > I am probably doing something really stupid, but I have searched the web and > the mailing lists and have so far not been able to solve my problem. My > overall aim is to run gcrma on custom affy arrays. As part of this I have > been looking at matchprobes and makecdfenv packages. I can successuly use > make.cdf.env and make.cdf.package. The trouble I am having is in trying to > install my new CDF package. The output of make.cdf.package is a directory > which i have then tried to zip up using winzip, in order to use the install > from local zipped file option. when i do this i get the following error > message. Yeah. That won't work. Here is the message you get from make.cdf.package() in the devel version of makecdfenv (suggested by Seth Falcon): README PLEASE: A source package has now been produced in c:/Documents and Settings/Jim/Desktop/CDF and probetabs/cdfs/agcdf. Before using this package it must be installed via 'R CMD INSTALL' at a terminal prompt (or DOS command shell). If you are using Windows, you will need to get set up to install packages. See the 'R Installation and Administration' manual, specifically Section 6 'Add-on Packages' as well as 'Appendix E: The Windows Toolset' for more information. Alternatively, you could use make.cdf.env(), which will not require you to install a package. However, this environment will only persist for the current R session unless you save() it. > >>make.cdf.package("XYZ.cdf",species = "Homo_sapiens") > > Creating package in C:/R/custom/xyzcdf > [1] "xyzcdf" > >>utils:::menuInstallLocal() > > Error in gzfile(file, "r") : unable to open connection > In addition: Warning messages: > 1: error -1 in extracting from zip file > 2: cannot open compressed file 'xyzcdf/DESCRIPTION' > > I was hoping to install the custom cdf as a package so that I could run > makeProbePackage. When I run makeProbePackage, I get the following error > > XYZ = make.cdf.env("XYZ.cdf") > makeProbePackage("XYZ", > datafile = gzfile("XYZ_probes.txt", open="r"), > outdir = outdir, > maintainer = "me" > version = "0.0.1", > species = "Homo_sapiens", > check = FALSE, > force = TRUE) > Importing the data. > Error in library("xyzcdf") : there is no package called 'xyzcdf' > Any pointers as to wehre I am going wrong and how i can resolve this would > be great. As noted above, you are not installing the cdf package correctly. You don't technically need the cdf package to be installed to build the probe package. You just need to set the comparewithcdf argument to FALSE. However, it is not a bad idea to compare the probe package and cdf to make sure things line up correctly. Best, Jim > Many thanks > > claire > > sessionInfo() > R version 2.5.0 (2007-04-23) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United > Kingdom.1252;LC_MONETARY=English_United > Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > "datasets" "methods" "base" > > other attached packages: > hgu133plus2cdf matchprobes simpleaffy genefilter > survival makecdfenv affy affyio Biobase > "1.16.0" "1.8.1" " 2.10.31" "1.14.1" > "2.31" > "1.14.0" "1.14.1" "1.4.0" "1.14.0" > > [[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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.