Entry: MAplot
Aliases: MAplot MAplot,PLMset-method
Keywords: hplot
Description: Relative M vs. A plots
URL: ../../../library/affyPLM/html/MAplot.html

Entry: PLMset-class
Aliases: PLMset-class PLMset weights<- coefs coefs<- se se<- coefs.probe coefs.const se.probe se.const Mbox normvec varcov residSE resid<- residuals<- indexProbesProcessed model.description sampleNames<- coefs,PLMset-method weights<-,PLMset-method weights,PLMset-method coefs<-,PLMset-method se,PLMset-method se<-,PLMset-method coefs.probe,PLMset-method coefs.const,PLMset-method se.probe,PLMset-method se.const,PLMset-method Mbox,PLMset-method image,PLMset-method show,PLMset-method boxplot,PLMset-method getCdfInfo,PLMset-method indexProbes,PLMset,character-method cdfName,PLMset-method normvec,PLMset-method resid,PLMset-method residuals,PLMset-method resid<-,PLMset-method residuals<-,PLMset-method residSE,PLMset-method varcov,PLMset-method indexProbesProcessed,PLMset-method model.description,PLMset-method summary,PLMset-method sampleNames,PLMset-method sampleNames<-,PLMset,character-method annotation,PLMset-method description,PLMset-method phenoData,PLMset-method phenoData<-,PLMset,AnnotatedDataFrame-method pData,PLMset-method pData<-,PLMset,data.frame-method nuse NUSE RLE nuse,PLMset-method NUSE,PLMset-method RLE,PLMset-method
Keywords: classes
Description: Class PLMset
URL: ../../../library/affyPLM/html/PLMset-class.html

Entry: PLMset2exprSet
Aliases: PLMset2exprSet pset2eset
Keywords: manip
Description: Convert a PLMset to an exprSet
URL: ../../../library/affyPLM/html/PLMset2exprSet.html

Entry: ReadRMAExpress
Aliases: ReadRMAExpress
Keywords: manip
Description: Read RMAExpress computed expression values
URL: ../../../library/affyPLM/html/ReadRMAExpress.html

Entry: internal functions
Aliases: bg.correct.shift bg.correct.stretch bg.correct.gcrma get.background.code get.normalization.code get.psi.code get.summary.code get.default.psi.k convert.LESN.param PLM.designmatrix PLM.designmatrix2 fitPLM.old PLM.designmatrix3 verify.bg.param verify.constraint.types verify.model.param verify.norm.param verify.output.param verify.variable.types normalize.AffyBatch.quantiles.chromosome
Keywords: internal
Description: Internal affyPLM functions
URL: ../../../library/affyPLM/html/affyPLM-internal.html

Entry: bg.correct.LESN
Aliases: bg.correct.LESN
Keywords: manip
Description: LESN - Low End Signal is Noise Background corrections
URL: ../../../library/affyPLM/html/bg.correct.LESN.html

Entry: fitPLM
Aliases: fitPLM
Keywords: manip
Description: Fit a Probe Level Model to Affymetrix Genechip Data.
URL: ../../../library/affyPLM/html/fitPLM.html

Entry: normalize.ExpressionSet
Aliases: normalize.ExpressionSet.quantiles normalize.ExpressionSet.loess normalize.ExpressionSet.contrasts normalize.ExpressionSet.qspline normalize.ExpressionSet.invariantset normalize.ExpressionSet.scaling normalize.ExpressionSet.methods
Keywords: manip
Description: Normalization applied to ExpressionSets
URL: ../../../library/affyPLM/html/normalize.exprSet.html

Entry: normalize.quantiles.probeset
Aliases: normalize.AffyBatch.quantiles.probeset
Keywords: manip
Description: Quantile Normalization applied to probesets
URL: ../../../library/affyPLM/html/normalize.quantiles.probeset.html

Entry: normalize.scaling
Aliases: normalize.scaling normalize.AffyBatch.scaling
Keywords: manip
Description: Scaling normalization
URL: ../../../library/affyPLM/html/normalize.scaling.html

Entry: preprocess
Aliases: preprocess
Keywords: manip
Description: Background correct and Normalize
URL: ../../../library/affyPLM/html/preprocess.html

Entry: pseudo.coloring
Aliases: pseudoColorBar pseudoPalette
Keywords: manip
Description: Coloring pseudo chip images
URL: ../../../library/affyPLM/html/pseudo.html

Entry: rmaPLM
Aliases: rmaPLM
Keywords: manip
Description: Fit a RMA to Affymetrix Genechip Data as a PLMset
URL: ../../../library/affyPLM/html/rmaPLM.html

Entry: threestep
Aliases: threestep
Keywords: manip
Description: Three Step expression measures
URL: ../../../library/affyPLM/html/threestep.html

Entry: threestepPLM
Aliases: threestepPLM
Keywords: manip
Description: Three Step expression measures returned as a PLMset
URL: ../../../library/affyPLM/html/threestepPLM.html