[BioC] tilingArray - problem calculating confidence intervals

[Krys Kelly]

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 at 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

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