Hi all, I have this problem if I normalize with invariant set method and compute expression whit li.wong method whit a plob and also whit a celcontainer: > p<-ReadAffy() reading CDF file processing information reading 6 CEL files...... preparing probe level object > nor2<-normalize(p, method="invariantset") > ex2<-express(nor2, normalize=F, summary.stat=li.wong) Background correcting Preparing Data Computing expression. This may take a while. Error in while (change > delta & iter < maxit) { : missing value where logical needed > ex2<-express(nor2, normalize=F, summary.stat=li.wong, maxit=1) Background correcting Preparing Data Computing expression. This may take a while. Error in while (change > delta & iter < maxit) { : missing value where logical needed or whit a celcontainer normalized whit liwong ex1 <- generateExprSet(list.norm, cdf, "liwong") 22283 ids to go process... instancianting an exprSet... . Error in while (change > delta & iter < maxit) { : missing value where logical needed I have this problem whit the stable release 1.0 on a win2k and on a redhat 7.3 (1Gb ram) and whit the developmental version on a win2k and a redhat 7.2 (1Gb ram). Why? Thanks __________________________________ Remo Sanges BioGeM Gene Expression Core Lab Via Pietro Castellino 111 80131 Naples Italy +39 081 6132265 sanges@biogem.it sanges@iigb.na.cnr.it __________________________________

our implementation of the li and wong procedure is not stable. the most common problem is that the code assumes the number of outliers wont cause certain variables to be NAs. this is quite common when the number of arrays is small. notice li and wong suggest at least 10 arrays for their procedure to work properly. what happens if you run express with the remove.outliers=F ? if that works, the you might be able to get it to work by adding a line like this if(length(change)==0) | is.na(change)) change <- 0 in the function fit.li.wong after every definition of "change". rafael On Tue, 10 Sep 2002, Remo Sanges wrote: > Hi all, > > I have this problem if I normalize with invariant set method and compute > expression whit li.wong method whit a plob and also whit a celcontainer: > > p<-ReadAffy() > > reading CDF file > processing information > reading 6 CEL files...... > preparing probe level object > > > nor2<-normalize(p, method="invariantset") > > > ex2<-express(nor2, normalize=F, summary.stat=li.wong) > Background correcting > Preparing Data > Computing expression. This may take a while. > Error in while (change > delta & iter < maxit) { : > missing value where logical needed > > > ex2<-express(nor2, normalize=F, summary.stat=li.wong, maxit=1) > Background correcting > Preparing Data > Computing expression. This may take a while. > Error in while (change > delta & iter < maxit) { : > missing value where logical needed > > > or whit a celcontainer normalized whit liwong > > ex1 <- generateExprSet(list.norm, cdf, "liwong") > 22283 ids to go process... > instancianting an exprSet... > . Error in while (change > delta & iter < maxit) { : > missing value where logical needed > > I have this problem whit the stable release 1.0 on a win2k and on a redhat > 7.3 (1Gb ram) and whit the developmental version on a win2k and a redhat 7.2 > (1Gb ram). > Why? > Thanks > > > __________________________________ > Remo Sanges > BioGeM > Gene Expression Core Lab > Via Pietro Castellino 111 > 80131 Naples > Italy > +39 081 6132265 > sanges@biogem.it sanges@iigb.na.cnr.it > __________________________________ > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >