I am using R2.3.1. I am trying to run the package tilingArray following the information in the vignette, "The segment function to fit a piecewise constant curve", and the "Segmentation demo". I downloaded tilingArray and allthe necessary packages from the Bioconductor website last week. I could not find any reference to my problem in the archive. When I try to calculate the confidence intervals, I get the message Error: could not find function "confint.breakpointsfull" The script and output are copied below. I will be grateful for any help. Thanks Krys > library(tilingArray) 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 > > INFILE <- "RH_i_vs_cell.txt" > array <- read.table(INFILE, header=TRUE) > > maxseg <- 500 > maxk <- 150 > seg <-segment(array$value, maxk=maxk, maxseg=maxseg) > > # Get the confidence intervals > segCI <- confint(seg, parm=111, level=0.95) Error: could not find function "confint.breakpointsfull" 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

Hi Wolfgang I realized I should give you more detailed information including the sessionInfo() from your response to another posting I made. I have attached the code I used for the "Segmentation demo" i.e. using the davidTiling data. I have pasted the output from my terminal session including the sessionInfo() below. The information I sent in my original posting was for my own data. Thanks for your help. Krys > source("C:/Documents and Settings/Krys/Desktop/Segmentation demo/Stuff for Wolfgang/SegmentationDemoConfintCode.R") Creating a variable with unnormalized data Selecting the probes in along-chromosome order Avoid oversampling Call the segmentation algorithm Calculate confidence intervals Error: could not find function "confint.breakpointsfull" > 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" -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Krys Kelly Sent: 11 September 2006 15:44 To: bioconductor at stat.math.ethz.ch Subject: [BioC] tilingArray - problem calculating confidence intervals I am using R2.3.1. I am trying to run the package tilingArray following the information in the vignette, "The segment function to fit a piecewise constant curve", and the "Segmentation demo". I downloaded tilingArray and allthe necessary packages from the Bioconductor website last week. I could not find any reference to my problem in the archive. When I try to calculate the confidence intervals, I get the message Error: could not find function "confint.breakpointsfull" The script and output are copied below. I will be grateful for any help. Thanks Krys > library(tilingArray) 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 > > INFILE <- "RH_i_vs_cell.txt" > array <- read.table(INFILE, header=TRUE) > > maxseg <- 500 > maxk <- 150 > seg <-segment(array$value, maxk=maxk, maxseg=maxseg) > > # Get the confidence intervals > segCI <- confint(seg, parm=111, level=0.95) Error: could not find function "confint.breakpointsfull" 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