library(simpleaffy)
setQCEnvironment("hgu133acdf") # no CDF corresponding to tag array
if ( require("mvoutData") ) {
data(s12c)
data(s12cQC)
data(s12cDEG)
library(affyPLM)
s12cPset = fitPLM(s12c)
ao = ArrayOutliers(s12c, alpha=0.05, qcOut=s12cQC, plmOut=s12cPset, degOut=s12cDEG)
ao
}
if (require("lumiBarnes")) {
library(lumiBarnes)
data(lumiBarnes)
ArrayOutliers(lumiBarnes, alpha=0.05)
lb2 = lumiBarnes
exprs(lb2)[1:20000,1:2] = 10000*exprs(lb2)[1:20000,1:2]
ArrayOutliers(lb2, alpha=0.05)
}
data(maqcQA) # affy
ArrayOutliers(maqcQA[,-c(1:2)], alpha=.05)
ArrayOutliers(maqcQA[,-c(1:2)], alpha=.01)
data(ilmQA) # illumina
ArrayOutliers(data.frame(ilmQA), alpha=.01)
data(itnQA) # 507 arrays from ITN
ArrayOutliers(itnQA, alpha=.01)
Run the code above in your browser using DataLab