[BioC] probe file for custom array

[James W. MacDonald]

Hi Lana,

Is this a PM-only chip?

Jim



Lana Schaffer wrote:
> 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

-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623