[BioC] the issue with analysis of multi-channel screen

[Ning]

Hi Wolfgang,

I have 3 channels applied in screen. Two of them are used as the reporter to
monitor the early stage of signaling pathway, the other one is for the late
stage. The following is the script

library("cellHTS2")
experimentName <- "DataIntegration"
dataPath <- system.file(experimentName, package="cellHTS2")
x <- readPlateList("Platelist.txt",
                    name=experimentName,
                    path=dataPath)
x <- configure(x,
               descripFile="Description.txt",
               confFile="Plateconf.txt",
               logFile="Screenlog.txt",
               path=dataPath)
negCtr <- vector("character", length=dim(Data(x))[3])
negCtr[1] <- "(?i)^ntc2-lps$"
negCtr[2] <- "(?i)^ntc2-lps$"
negCtr[3] <- "(?i)^ntc2-lps$" 
posCtrs <- vector("character", length=dim(Data(x))[3])
posCtrs[1] <- list(act="(?i)^ntc2+lps$", inh="(?i)^myd88$|^tlr4$|^irak1+4$")
posCtrs[2] <- list(act="(?i)^ntc2+lps$", inh="(?i)^myd88$|^tlr4$|^irak1+4$")
posCtrs[3] <- list(act="(?i)^ntc2+lps$", inh="(?i)^myd88$|^tlr4$|^irak1+4$")   
         
xn <- normalizePlates(x,
                      scale="multiplicative",
                      log=FALSE,
                      method="median",
                      varianceAdjust="none")
xsc <- scoreReplicates(xn, sign="+", method="zscore")
xsc <- summarizeReplicates(xsc, summary="median")

However, when I checked the state by calling state(xsc), the result showed XSC
has not been scored. When I checked the xsc data by using Data(xsc), it showed
the z score has been calculated. Do you have any idea about it? 

Many thanks

Ning

sessionInfo()
cellHTS2 
R version 2.11.1(2010-05-31)