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),estima te="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

There may be an easier way, but this worked for me as of last month - dunno if functions changed since. # Grp.AB is an Affybatch object Grp.pm.mtx <- pm(Grp.AB) Grp.mm.mtx <- mm(Grp.AB) Grp.GroupInfo <-getGroupInfo(Grp.AB) Grp.pm.gcbgc.eb.mtx <- do.call("cbind", lapply(X=1:ncol(Grp.pm.mtx), FUN=function(jj) bg.adjust.gcrma( Data = array(c(Grp.pm.mtx[, jj], Grp.mm.mtx[, jj]), dim=c(nrow(Grp.pm.mtx), 2)), gcgroup=Grp.GroupInfo, estimate="eb", triple.goal=F))) -franncois Jenny Drnevich <drnevich@uiuc.edu> Sent by: bioconductor-bounces@stat.math.ethz.ch 10/31/03 01:19 PM To: bioconductor@stat.math.ethz.ch cc: Subject: [BioC] help w/ bg.correct.gcrma 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 [[alternative HTML version deleted]]