Hi Lana, I doubt you can put in fake MM probes for the GC probes. Does this chip really have MM probes, or does it have genomic and antigenomic probes that are used instead of MM probes (of which I would assume the GC probes are a part)? There may be a way to hack things to work, but the best person to ask would be Zhijin Wu, the maintainer of gcrma (If you in fact are intending to use gcrma. Another assumption on my part since you don't say what you are really trying to do.). Anyway, I don't think faking things is the answer. Best, Jim Lana Schaffer wrote: > 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 at 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 -- 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

Jim, Affy made for me a new CDF file with only PM and no MM's. Now when making a probe package I am getting again a similar error: Importing the data. Attaching package: 'glycov3hscdf' The following object(s) are masked from package:glycov3hspmcdf : i2xy, xy2i Error in rep(NA, max(pm1, mm1, pm2, mm2)) : invalid 'times' argument Looks like they are looking for MM's. The chip has antigenomic probes (GC bins) and MM's for the human/mouse genes. I will be trying to use the Fischer Combined P value method to evaluate expressed/not expressed genes on the custom chip and using the PM probe sets. Lana -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Monday, March 03, 2008 7:59 AM To: Lana Schaffer Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] probe file for custom array Hi Lana, I doubt you can put in fake MM probes for the GC probes. Does this chip really have MM probes, or does it have genomic and antigenomic probes that are used instead of MM probes (of which I would assume the GC probes are a part)? There may be a way to hack things to work, but the best person to ask would be Zhijin Wu, the maintainer of gcrma (If you in fact are intending to use gcrma. Another assumption on my part since you don't say what you are really trying to do.). Anyway, I don't think faking things is the answer. Best, Jim Lana Schaffer wrote: > 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 at 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 -- 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

Jim, I just wanted to get the sequence of the probes and the GC content. Looks like I don't need to use matchprobes and just write/find the function to get the GC content. I get that matchprobes assumes MM probes exist. Lana -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Monday, March 03, 2008 7:59 AM To: Lana Schaffer Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] probe file for custom array Hi Lana, I doubt you can put in fake MM probes for the GC probes. Does this chip really have MM probes, or does it have genomic and antigenomic probes that are used instead of MM probes (of which I would assume the GC probes are a part)? There may be a way to hack things to work, but the best person to ask would be Zhijin Wu, the maintainer of gcrma (If you in fact are intending to use gcrma. Another assumption on my part since you don't say what you are really trying to do.). Anyway, I don't think faking things is the answer. Best, Jim Lana Schaffer wrote: > 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 at 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 -- 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