useDynLib(beadarray)
import(Biobase)

importFrom(hwriter, closePage, hwrite, openPage)

importClassesFrom(limma, RGList)
importFrom(limma, normalizeQuantiles, normexp.fit, normexp.signal)

exportClasses(ExpressionSetIllumina, BeadLevelList)
exportMethods(initialize, show,se.exprs, exprs, "[","[[","$", phenoData, pData,sampleNames,samples, "se.exprs<-","exprs<-", "NoBeads<-", "Detection<-", "QCInfo<-", dim, assayData, initialize, NoBeads, Detection, backgroundCorrect, QCInfo, copyBeadLevelList, combineBeadLevelLists, getProbeIntensities, getArrayData, arrayNames, numBeads, getVariance, combine)


export(SAMSummary, BeadChipSummary, medianNormalise, rankInvariantNormalise, plotBeadIntensities, plotBeadLocations, imageplot, plotMAXY, plotMA, plotRG, plotXY, plotOnSAM, readQC, readIllumina, readBeadSummaryData, findBeadStatus, boxplotBeads, createBeadSummaryData, findAllOutliers, qcBeadLevel, plotBeadDensities, beadResids, readBGX, normaliseIllumina, setWeights, beadarrayUsersGuide, addArrayMask, removeArrayMask, clearArrayMask, showArrayMask, BASH, BASHCompact, BASHDiffuse, BASHExtended, generateE, generateNeighbours, BGFilter, BGFilterWeighted, chooseClusters, closeImage, denseRegions, viewBeads,getAnnotation,setAnnotation,getControlAnno,calculateDetection,calculateBeadLevelScores,probePairsPlot,lmhPlot,backgroundControlPlot,poscontPlot,gradientPlot, outlierPlot, HULK, HULKResids, readTIFF, plotTIFF, readLocs)
