error with getMeasureRepAgreement() Hi, I want to use "pearson" rather than "spearman". So I made such a change: xsc <- getMeasureRepAgreement(xn, corr.method = "pearson") However an error happened: Error in cellHTSlistVerification (xr = raw, xn = normalized, xsc = scored, : The component 'scored' of 'cellHTSlist' should be a 'cellHTS' object containing scored data! Please check its preprocessing state: configured = TRUE, normalized = TRUE, scored = FALSE, annotated = TRUE Does anyone have any ideas about it? Many thanks! Ning sessionInfo() cellHTS2 R version 2.11.1(2010-05-31) The following is the code: experimentName <- "mcherry" 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) xn <- normalizePlates(x, scale="multiplicative", log=FALSE, method="NPI", varianceAdjust="none") xsc <- getMeasureRepAgreement(xn, corr.method = "pearson") xsc <- scoreReplicates(xn, sign="-", method="zscore") xsc <- summarizeReplicates(xsc, summary="median") xsc <- annotate(xn, geneIDFile="GeneIDs.txt", path=dataPath) setSettings(list(plateList=list(reproducibility=list(include=TRUE, map=TRUE), intensities=list(include=TRUE, range=c(-0.5,1), map=TRUE)), screenSummary=list(scores=list(range=c(-4, 8), map=TRUE)))) out <- writeReport(raw=x, normalized=xn, scored=xsc,map=TRUE,outdir="C:\\Documents and Settings\\lin6\\Desktop\\R\\mcherry",force=TRUE) browseURL(out)

Dear Ning, thank you for the code example. I think the problem lies in the line xsc <- annotate(xn, geneIDFile="GeneIDs.txt", path=dataPath) which you execute *after* computing the scored and summarised xsc, hence in effect overwriting it. In fact, the error message seems to be quite descriptive of the problem (which btw it seems has nothing to do with your choice of corr.method = "pearson"). For next time, I suggest: - make your example reproducible (the directory/dataset "mcherry" is private to your computer). - mention the name of the package (cellHTS2) in the subject line or somewhere prominent. Also note that the example datasets that come with the cellHTS2 package are stored in within the package, hence the dataPath = system.file(experimentName, package="cellHTS2"), but you can put your own data whereever you like on the file system, just set "dataPath" accordingly. Best wishes Wolfgang Ning scripsit 10/08/10 22:46: > error with getMeasureRepAgreement() > > > Hi, > I want to use "pearson" rather than "spearman". So I made such a change: > xsc<- getMeasureRepAgreement(xn, corr.method = "pearson") > However an error happened: > Error in cellHTSlistVerification (xr = raw, xn = normalized, xsc = scored, : > The component 'scored' of 'cellHTSlist' should be a 'cellHTS' object > containing scored data! > Please check its preprocessing state: configured = TRUE, normalized = TRUE, > scored = FALSE, annotated = TRUE > Does anyone have any ideas about it? > > Many thanks! > > Ning > > > sessionInfo() > cellHTS2 > R version 2.11.1(2010-05-31) > > The following is the code: > > experimentName<- "mcherry" > 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) > xn<- normalizePlates(x, > scale="multiplicative", > log=FALSE, > method="NPI", > varianceAdjust="none") > xsc<- getMeasureRepAgreement(xn, corr.method = "pearson") > xsc<- scoreReplicates(xn, sign="-", method="zscore") > xsc<- summarizeReplicates(xsc, summary="median") > xsc<- annotate(xn, geneIDFile="GeneIDs.txt", > path=dataPath) > setSettings(list(plateList=list(reproducibility=list(include=TRUE, map=TRUE), > intensities=list(include=TRUE, range=c(-0.5,1), map=TRUE)), > screenSummary=list(scores=list(range=c(-4, 8), map=TRUE)))) > out<- writeReport(raw=x, normalized=xn, > scored=xsc,map=TRUE,outdir="C:\\Documents and > Settings\\lin6\\Desktop\\R\\mcherry",force=TRUE) > browseURL(out) > > _______________________________________________ > 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 EMBL http://www.embl.de/research/units/genome_biology/huber