Hi,
 
We would like to use gcrma for our custom Affymetrix array (no mismatch
probes; only perfect match probes). I have successfullly created the CDF
package in Bioconductor. Now I need to create the probe package with the
function makeProbePackage().
 
I executed the following command:
 
makeProbePackage("ourchip", datafile="ourchip_probeSequence_6cols.txt",
outdir= getwd(), maintainer="our name<ouremail@ucdavis.edu>",
version="0.0.1", species="Our species", check=FALSE, force=TRUE,
quiet=FALSE)
 
Note: I did experiment with the parameters 'check, 'force' and 'quiet', but
it gave the same result. The output was as follows:
 
Importing the data.
Error in rep.default(NA, max(pm1, mm1, pm2, mm2)) : 
        invalid number of copies in rep()
 
I also tried calling the getProbeDataAffy() function explicitly, like this:
 
makeProbePackage("ourchip", getProbeDataAffy("ourchip",
"ourchip_probeSequence_6cols.txt", pkgname=NULL, comparewithcdf=TRUE),
outdir= getwd(), maintainer="our name<ouremail@ucdavis.edu>",
version="0.0.1", species="Our species", check=FALSE, force=TRUE,
quiet=FALSE)
 
But it resulted in the same error. I have searched online and in the
Bioconductor archives for this error, and the only thread was this one:
https://stat.ethz.ch/pipermail/bioconductor/2005-September/010249.html
 
Unfortunately, no solution was suggested in that thread. 
 
Does anyone know what the problem is, and how this can be solved? I suspect
that it has to do with the input file that I have created. However, I used
the example templates from Bioconductor, so in theory it should be okay. I
have six columns in my file, with the following headers:
 
Probe Set Name
Probe X
Probe Y
Probe Interrogation Position
Probe Sequence
Target Strandedness
 
The header fields, and all the data, is seperated with tabs. Each row has
data for one probe; rows are seperated by a newline character. Within the
header fields there are spaces.
 
Is the problem related to the fact that our array does not have mismatch
probes? Can gcrma() be used with arrays that do not have mismatch probes?
 
I would be very grateful if someone can help with this.
 
Thank you.
 
Hans
 

 

____________________________________

Hans van Leeuwen, Ph.D.

University of California, Davis


 <http://pgfmars.ucdavis.edu/~hleeuwen/> 

 


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