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)

Ning, it seems that the function "scoreReplicates" does not mark the fact that scoring has been done in the "state" of the object, but does so in the "processingInfo" slot. (Type "scoreReplicates" without parentheses to see its simple code.) Florian Hahne might be able to give a deeper answer, but it seems he's currently entertaining two partially redundant history keeping mechanisms in the cellHTS class. I think they are for information only and do not influence the computed results. Otherwise, your code looks great, I hope you find the package useful and get good results out of it. Let us know if you have questions. Best wishes Wolfgang Il Oct/22/10 11:12 PM, Ning ha scritto: > 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) > > _______________________________________________ > 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