[BioC] error with getMeasureRepAgreement()

[Ning]

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)