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

[andrew.w.wooster at gsk.com]

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
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> 
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-- 
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



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