The first try should read like this: bgaffy <-bg.correct.gcrma(rawaffy,gcgroup=getGroupInfo(rawaffy),estimate="eb" , triple.goal=TRUE) Note the error in your message. You can also set triple.goal=FALSE, but you have to do one or the other. As for the multi-argument returns message, that is simply a change as of R-1.8.0 that really only concerns the package maintainer. For now the functions will work fine (except for the annoying warnings). HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Jenny Drnevich <drnevich@uiuc.edu> 10/31/03 16:29 PM >>> Hi, I want to explore the GC-based background correction in gcrma. I'd like to get the bg corrected PM values, not the summary values. I think I can do this with bg.correct.gcrma, but I'm having problems getting it to run correctly. I'm looking at some of the Affy spike-in data, and running R 1.8.0 and Bioconductor 1.3. I followed the format I found from ?bg.correct.gcrma: > bgaffy <-bg.correct.gcrma(rawaffy,gcgroup=getGroupInfo(rawaffy),estimate="eb" ) Loading required package: hgu95aprobe Loading required package: matchprobes Error in FUN(array(newX[, i], d.call, dn.call), ...) : Argument "triple.goal" is missing, with no default In addition: Warning messages: 1: multi-argument returns are deprecated in: return(y = yhat, wt) 2: multi-argument returns are deprecated in: return(y = yhat, wt) 3: multi-argument returns are deprecated in: return(y = yhat, wt) 4: multi-argument returns are deprecated in: return(y = yhat, wt) 5: multi-argument returns are deprecated in: return(y = yhat, wt) Additionally, I tried: bgaffy <-bg.correct.gcrma(rawaffy,gcgroup=getGroupInfo(rawaffy),estimate="mle ") and got over 50 of the "multi-argument returns" warning messages. Any ideas about what I need to do? Thanks, Jenny Jenny Drnevich, Ph.D. Department of Animal Biology 515 Morrill Hall 505 S Goodwin Ave Urbana, IL 61801 USA ph: 217-244-6826 fax: 217-244-4565 e-mail: drnevich@uiuc.edu _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Thanks, James. I will update the "return" line in gcrma to be compatible with R-1.8. Jean ----- Original Message ----- From: James MacDonald <jmacdon@med.umich.edu> Date: Friday, October 31, 2003 9:17 pm Subject: Re: [BioC] help w/ bg.correct.gcrma > The first try should read like this: > > bgaffy > <- > bg.correct.gcrma(rawaffy,gcgroup=getGroupInfo (rawaffy),estimate="eb",triple.goal=TRUE) > > Note the error in your message. You can also set > triple.goal=FALSE, but > you have to do one or the other. > > As for the multi-argument returns message, that is simply a change > as of > R-1.8.0 that really only concerns the package maintainer. For now the > functions will work fine (except for the annoying warnings). > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > >>> Jenny Drnevich <drnevich@uiuc.edu> 10/31/03 16:29 PM >>> > Hi, > > I want to explore the GC-based background correction in gcrma. I'd > liketo > get the bg corrected PM values, not the summary values. I think I > can do > > this with bg.correct.gcrma, but I'm having problems getting it to > run > correctly. I'm looking at some of the Affy spike-in data, and > running R > 1.8.0 and Bioconductor 1.3. I followed the format I found from > ?bg.correct.gcrma: > > > bgaffy > <- > bg.correct.gcrma(rawaffy,gcgroup=getGroupInfo(rawaffy),estimate="eb") Loading required package: hgu95aprobe > Loading required package: matchprobes > Error in FUN(array(newX[, i], d.call, dn.call), ...) : > Argument "triple.goal" is missing, with no default > In addition: Warning messages: > 1: multi-argument returns are deprecated in: return(y = yhat, wt) > 2: multi-argument returns are deprecated in: return(y = yhat, wt) > 3: multi-argument returns are deprecated in: return(y = yhat, wt) > 4: multi-argument returns are deprecated in: return(y = yhat, wt) > 5: multi-argument returns are deprecated in: return(y = yhat, wt) > > Additionally, I tried: > > bgaffy > <- > bg.correct.gcrma(rawaffy,gcgroup=getGroupInfo(rawaffy),estimate="mle") > and got over 50 of the "multi-argument returns" warning messages. Any > ideas > about what I need to do? > > Thanks, > Jenny > > > Jenny Drnevich, Ph.D. > Department of Animal Biology > 515 Morrill Hall > 505 S Goodwin Ave > Urbana, IL 61801 > USA > > ph: 217-244-6826 > fax: 217-244-4565 > e-mail: drnevich@uiuc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >