Jim, This chip is not a PM only but contain MM also. Lana -----Original Message----- From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Thursday, June 07, 2007 12:03 PM To: Lana Schaffer Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] mas5calls with make.cdf.env Lana Schaffer wrote: > Jim, > GCOS is making the mas5calls with these CDF files. I'm confused. Does that mean it is or is not a PM-only chip? > Lana > > -----Original Message----- > From: James W. MacDonald [mailto:jmacdon at med.umich.edu] > Sent: Thursday, June 07, 2007 11:20 AM > To: Lana Schaffer > Cc: bioconductor at stat.math.ethz.ch > Subject: Re: [BioC] mas5calls with make.cdf.env > > Looks to me like you might have a PM-only chip. Is this the case? > > Best, > > Jim > > Lana Schaffer wrote: > >>James, >> >> >>>sessionInfo() >> >>R version 2.5.0 (2007-04-23) >>i386-pc-mingw32 >> >>locale: >>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>States.1252;LC_MONETARY=English_United >>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >>attached base packages: >>[1] "tools" "stats" "graphics" "grDevices" "utils" >>"datasets" >>[7] "methods" "base" >> >>other attached packages: >>makecdfenv affy affyio Biobase >> "1.14.0" "1.14.0" "1.4.0" "1.14.0" >> >> >> >>>traceback() >> >>7: .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, x]), >> as.character(pns), as.integer(length(mms[, x])), > > as.double(tau), > >> as.double(sat), dpval = double(length(unique.pns)), >>length(unique.pns), >> PACKAGE = "affy") >>6: FUN(1:6[[1L]], ...) >>5: lapply(X, FUN, ...) >>4: sapply(1:length(pms[1, ]), function(x) { >> .C("DetectionPValue", as.double(pms[, x]), as.double(mms[, >> x]), as.character(pns), as.integer(length(mms[, x])), >> as.double(tau), as.double(sat), dpval = >>double(length(unique.pns)), >> length(unique.pns), PACKAGE = "affy")$dpval >> }) >>3: mas5calls.AffyBatch(object, ...) >>2: mas5calls(abatch) >>1: mas5calls(abatch) >> >>Thanks, >>Lana >> >> >> >> >>-----Original Message----- >>From: James W. MacDonald [mailto:jmacdon at med.umich.edu] >>Sent: Thursday, June 07, 2007 6:19 AM >>To: Lana Schaffer >>Cc: bioconductor at stat.math.ethz.ch >>Subject: Re: [BioC] mas5calls with make.cdf.env >> >>Hi Lana, >> >>Lana Schaffer wrote: >> >> >>>Hi James, >>>R version 2.5.0 (2007-04-23) >>>makecdfenv "1.14.0" >>>I am following the vignette for makecdfenv to create a new cdfenv and >>>can use this env for functions llike plotHist but I get an error when >>>using the function mas5calls. >>>Error: >>>Getting probe level data... >>>Computing p-values >>>Error in FUN(1:6[[1L]], ...) : NA/NaN/Inf in foreign function call >>>(arg >>>2) >>>This is my code: >>>mycdfenv <- make.cdf.env("myname.CDF") abatch <- ReadAffy() >>>abatch at cdfName <- "mycdfenv" >>>Calls <-mas5calls(abatch) >>>-Error- >>>Can someone help me get the mas5calls function to work here? >> >> >>How about giving us a sessionInfo() and a traceback() after the error. >> >>Best, >> >>Jim >> >> >> >> >>>Thanks, >>> >>>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, 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 >> >> >>********************************************************** >>Electronic Mail is not secure, may not be read every day, and should >>not be used for urgent or sensitive issues. > > > > -- > 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 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues. -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.