Any idea? BTW, it works fine when I used unnormalized data. -michael ############################### > tmp <- normalize.Plob.invariantset(latin) # use the first CHIP as reference > latin.LiWong <- express(tmp, normalize=F, bg=subtractmm, 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 In addition: Warning message: No convergence in inner loop after 50 in outerler tieration 4 in: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, > latin.LiWong <- express(tmp, normalize=F, summary.stat=li.wong) Background correcting Error in density(x, kernel = "epanechnikov", n = n.pts) : x contains missing values > latin.avdf <- express(tmp,normalize=F,bg=subtractmm,summary.stat=avdiff) Background correcting Preparing Data Computing expression. This may take a while. Error in var(x, na.rm = na.rm) : missing observations in cov/cor > latin.avdf <- express(tmp,normalize=F,bg=subtractmm, + summary.stat=function(x) apply(x,2,mean,trim=.2)) Background correcting Preparing Data Computing expression. This may take a while. Error in psort(x, partial) : index 13 outside bounds

On Thu, Oct 17, 2002 at 11:24:24AM -0400, Man, Michael wrote: > Any idea? BTW, it works fine when I used unnormalized data. -michael Several even... which version of R and of the package are you using ? L. > > ############################### > > tmp <- normalize.Plob.invariantset(latin) # use the first CHIP as > reference > > latin.LiWong <- express(tmp, normalize=F, bg=subtractmm, > 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 > In addition: Warning message: > No convergence in inner loop after 50 in outerler tieration 4 > in: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, > > > > latin.LiWong <- express(tmp, normalize=F, summary.stat=li.wong) > Background correcting > Error in density(x, kernel = "epanechnikov", n = n.pts) : > x contains missing values > > > > latin.avdf <- express(tmp,normalize=F,bg=subtractmm,summary.stat=avdiff) > Background correcting > Preparing Data > Computing expression. This may take a while. > Error in var(x, na.rm = na.rm) : missing observations in cov/cor > > > > latin.avdf <- express(tmp,normalize=F,bg=subtractmm, > + summary.stat=function(x) apply(x,2,mean,trim=.2)) > Background correcting > Preparing Data > Computing expression. This may take a while. > Error in psort(x, partial) : index 13 outside bounds > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent

On Mon, Oct 21, 2002 at 09:23:16AM -0400, Tibor van Rooij wrote: > I have the exact same problem and I have used it on various data- sets which normalize well with the quantile method. > > I get the same errors as well. > > My guess is that it breaks on the NA that gets put in the pm matrix after the invariantset normalization. > > Tibor > _______________________________ > Tibor van Rooij > Bioinformatician > Montreal Genome Centre > McGill University, Duff Building > Tel: (514) 398-2497 > Fax: (514) 398-1838 > > ok... but still, having a look at the data to check where things go wrong would help L. -- -------------------------------------------------------------- Laurent Gautier CBS, Building 208, DTU PhD. Student DK-2800 Lyngby,Denmark tel: +45 45 25 24 89 http://www.cbs.dtu.dk/laurent