I should have included the code I'm using. Sorry. Here it is. My data are in mzData format.
Samples <- list.files(getwd(), pattern="mzdata.xml", full.names=FALSE, recursive=TRUE)
QCset <- xcmsSet(Samples, method = "centWave", snthresh = 10,
ppm=5, peakwidth=c(10,30),
mzCenterFun="wMean",integrate = 1,fitgauss= TRUE)
QCset
QCset.mzClust <- group(QCset, method="mzClust", minsamp=1, mzppm=5)
QCset.mzClust.2 <- retcor(QCset.mzClust, missing=0, extra=1, smooth="loess",
family="symmetric", plottype="mdevden")
QCset.mzClust.3 <- group(QCset.mzClust.2, method="mzClust", minsamp=1, mzppm=5)
QCset.mzClust.4 <- fillPeaks(QCset.mzClust.3)
QCset.5c1c <- diffreport(QCset.mzClust.4, "20110211", "20110223", "QCurine XCMS 5c1c", 20)
Laura