-----Original Message----- From: Man, Michael Sent: Thursday, October 17, 2002 1:57 PM To: Warnes, Gregory R Subject: RE: [BioC] can't get summary.stat after "invariantset" normalizat ion It's version 1.0. -m -----Original Message----- From: Warnes, Gregory R Sent: Thursday, October 17, 2002 1:16 PM To: Man, Michael Subject: RE: [BioC] can't get summary.stat after "invariantset" normalizat ion We will want to know which version of affy. To find out do 'library(help=affy)'. -Greg > -----Original Message----- > From: Man, Michael > Sent: Thursday, October 17, 2002 12:45 PM > To: 'Laurent Gautier' > Cc: 'bioconductor@stat.math.ethz.ch' > Subject: RE: [BioC] can't get summary.stat after "invariantset" > normalizat ion > > > R1.6 and Affy on IBM Thinkpad T22 . -m > > -----Original Message----- > From: Laurent Gautier [mailto:laurent@cbs.dtu.dk] > Sent: Thursday, October 17, 2002 12:27 PM > To: Man, Michael > Cc: 'bioconductor@stat.math.ethz.ch' > Subject: Re: [BioC] can't get summary.stat after "invariantset" > normalization > > > > 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 > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > LEGAL NOTICE Unless expressly stated otherwise, this message is confidential and may be privileged. It is intended for the addressee(s) only. Access to this E-mail by anyone else is unauthorized. If you are not an addressee, any disclosure or copying of the contents of this E-mail or any action taken (or not taken) in reliance on it is unauthorized and may be unlawful. If you are not an addressee, please inform the sender immediately.