[BioC] GCRMA computing affinities error length(prlen) == 1

[Zhijin Wu]

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 at 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 at 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 at med.umich.edu> 
> 05-Apr-2005 10:43
>  
> To
> andrew.w.wooster at gsk.com
> cc
> Bioconductor at stat.math.ethz.ch
> Subject
> Re: [BioC] Binary CDF file
> 
> 
> 
> 
> 
> 
> andrew.w.wooster at 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 at 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]]
> 
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