Jim, I think that is the problem. There are both MM probes for the species and there are GC probes for background calculations. I was wondering if I could put in fake MM probes for the GC probes?? Lana -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Friday, February 29, 2008 5:47 AM To: Lana Schaffer Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] probe file for custom array 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- > 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