Hi Wolfgang, I'm sorry I did not include specific information. I have attached my code. Below is the output from my terminal session, including the output from SessionInfo() at the end. I just downloaded a new version of R and all these packages last week, so they should be up-to-date (but maybe I missed something, or introduced an error in the code). Thanks for looking at this for me. Best wishes Krys > source("C:/Documents and Settings/Krys/Desktop/Segmentation demo/Stuff for Wolfgang/SegmentationDemoCode.R") Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Loading required package: affy Loading required package: affyio Loading required package: RColorBrewer Loading required package: grid Loading required package: strucchange Loading required package: zoo Loading required package: sandwich Loading required package: colorspace Attaching package: 'colorspace' The following object(s) are masked from package:grDevices : hcl Loading required package: vsn Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: geneplotter Loading required package: annotate KernSmooth 2.22 installed Copyright M. P. Wand 1997 Loading required package: GO Error in vsn(xn, lts.quantile = 0.95, subsample = 2e+05, verbose = verbose) : The likelihood optimization did not converge. A likely reason is that the normalization parameters are not uniquely identifiable from the provided data. Possibly, the columns of the data matrix are exactly co-linear or affine dependent - please verify the data to make sure there were no mix-ups. > session.info() Error: could not find function "session.info" > sessionInfo() Version 2.3.1 (2006-06-01) i386-pc-mingw32 attached base packages: [1] "splines" "grid" "tools" "methods" "stats" "graphics" [7] "grDevices" "utils" "datasets" "base" other attached packages: davidTiling GO tilingArray geneplotter annotate genefilter "1.0.4" "1.12.0" "1.10.0" "1.10.0" "1.10.0" "1.10.1" survival vsn colorspace strucchange sandwich zoo "2.28" "1.10.0" "0.9" "1.3-0" "2.0-0" "1.2-0" RColorBrewer affy affyio Biobase "0.2-3" "1.10.0" "1.0.0" "1.10.1" > Dr Krystyna A Kelly University of Cambridge Department of Pathology Molteno Building, Tennis Court Road Cambridge CB2 1QP Tel: 01223 333331 Email: kak28 at cam.ac.uk -----Original Message----- From: Wolfgang Huber [mailto:huber@ebi.ac.uk] Sent: 13 September 2006 10:46 To: Krys Kelly Cc: bioconductor at stat.math.ethz.ch Subject: Re: [BioC] Segmentation Demo - problem in normalization Dear Krys, please can you provide 1. a script that allows us to reproduce the error condition you get, and 2. the output of sessionInfo() Otherwise I am afraid your question is too unspecific to do anything about it. Best wishes Wolfgang Krys Kelly wrote: > I am trying to run the Segmentation Demo. I have been cutting and pasting > the commands from the Segmentation Demo document. > > I get an error during the normalization. When I run this command: > > xn = normalizeByReference(davidTiling[, isRNA], davidTiling[, isDNA], pm = > PMind, background = isbg) > > I get the following error message: > > The likelihood optimization did not converge. A likely reason is that the > normalization parameters are not uniquely identifiable from the provided > data. > Possibly, the columns of the data matrix are exactly co-linear or affine > dependent - please verify the data to make sure there were no mix- ups. > > Please can you help. > > Thanks > > Krys > > > Dr Krystyna A Kelly > University of Cambridge > Department of Pathology > Molteno Building, Tennis Court Road > Cambridge CB2 1QP > Tel: 01223 333331 > Email: kak28 at cam.ac.uk > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber