[BioC] probe file for custom array

[Lana Schaffer]

Jim,
I have installed the custom CDF package and still not able
to finish creating the probe package.  This is my error:
Importing the data.
Error in rep(NA, max(pm1, mm1, pm2, mm2)) : invalid 'times' argument 
Can you give me a hint to figure out the problem?  

> filename <- system.file("extdata",
"GLYCOv3_Hs_probeseqs.gz",package="matchprobes")
> outdir <- tempdir()
> me <- "Lana Schaffer <schaffer at scripps.edu>"
> species <- "homo_sapiens"
> makeProbePackage("glycov3Hs", datafile=gzfile(filename, open="r"), 
+ outdir=outdir,maintainer=me,species=species, version =
"0.0.1",force=TRUE)
Importing the data.
Error in rep(NA, max(pm1, mm1, pm2, mm2)) : invalid 'times' argument   
> sessionInfo()
R version 2.6.0 (2007-10-03) 
i386-pc-mingw32 

other attached packages:
 [1] glycov3hscdf_1.16.0  makecdfenv_1.16.0    simpleaffy_2.14.05  
 [4] genefilter_1.16.0    survival_2.32        affyPLM_1.14.0      
 [7] gcrma_2.10.0         matchprobes_1.10.0   affy_1.16.0         
[10] preprocessCore_1.0.0 affyio_1.6.0         Biobase_1.16.3      

   Lana
-----Original Message-----
From: James MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Tuesday, February 26, 2008 3:39 PM
To: Lana Schaffer
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] probe file for custom array

You get the probe_tab file from Affymetrix and then use
makeProbePackage() in the matchprobes package.

Best,

Jim



Lana Schaffer wrote:
> Hi,
> I would like to make a probe file for a custom array.  How do I do 
> this?
> 
> Lana Schaffer
> Biostatistics/Informatics
> The Scripps Research Institute
> DNA Array Core Facility
> La Jolla, CA 92037
> (858) 784-2263
> (858) 784-2994
> schaffer at scripps.edu
> 
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--
James W. MacDonald, MS
Biostatistician
UMCCC cDNA and Affymetrix Core
University of Michigan
1500 E Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623