andrew.w.wooster@gsk.com wrote: > > I am using version Bioconductor 1.5. How do I get the current devel > version of makecdfenv? Download R-2.1.0alpha, then use getBioC("affy", develOK=TRUE) -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

where do you get your probe package? try for example, probepkgname="hgu95aprobe" ###change this to your probe package name seq1=get(probepkgname) prlen=nchar(seq1$seq) range(prlen) you should get [1] 25 25 since affy probes are all 25-bases long. The error message you get seems to suggest that you have probes of other lengths On Wed, 6 Apr 2005 andrew.w.wooster@gsk.com wrote: > 1) I create my own cdf and probe packages from a .CDF file as follows: > > cdfName <- "RAE230A" > cdfFilename <- paste(cdfName,".CDF",sep=""); > > library(makecdfenv); > make.cdf.package(filename=cdfFilename); > > library(matchprobes); > makeProbePackage( > cdfName, > datafile=file(system.file(".",cdfFilename),open="r"), > maintainer="<andrew.w.wooster@gsk.com>", > version="0.0.1"); > > 2) I then run GCRMA as follows: > > library(gcrma); > justGCRMA(); > > 3) I get the following error: > > Computing affinities.Error: length(prlen) == 1 is not TRUE > > > The reason I create my own cdf and probe packages is because I have binary > .CDF file. I originally saw this problem using the binary file. I then > retried the steps above using the text RAE230A.CDF file - and got the same > error. > > I am using the developers version of Bioconductor, which I downloaded > yesterday April 5 2005 as follows: > getBioC("affy", develOK=TRUE) > > I do not get the error if I use the RAE230A packages from the Bioconductor > metadata repository. > > What am I missing? > > > > > "James W. MacDonald" <jmacdon@med.umich.edu> > 05-Apr-2005 10:43 > > To > andrew.w.wooster@gsk.com > cc > Bioconductor@stat.math.ethz.ch > Subject > Re: [BioC] Binary CDF file > > > > > > > andrew.w.wooster@gsk.com wrote: > > Does Bioconductor support binary .CDF files? > > > > When I attempt to make a CDF package ad follows: > > make.cdf.package("U133AAofAv2.CDF") > > > > I get the following error message: > > Error in getInfoInFile(file, "CDF", unit = "Chip", property = "Name", > : > > The file /home/aww35131/microarray/U133AAofAv2.CDF does not > appear > > to be a CDF file. > > The current devel version of makecdfenv does support binary .cdf files. > What version are you using? > > Jim > > > > > > -Andrew > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > 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 > 734-647-5623 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >