Entry: PairComp-class
Aliases: PairComp-class [,PairComp-method [<-,PairComp-method calls,PairComp-method fc,PairComp-method group,PairComp-method means,PairComp-method members,PairComp-method pairwise.filter,PairComp-method tt,PairComp-method pData,PairComp-method calculated.from,PairComp-method calls fc group means members tt pData calculated.from plot,PairComp,ANY-method
Keywords: classes
Description: Class "PairComp" Represents the results of pairwise comparison between two experimental factors
URL: ../../../library/simpleaffy/html/PairComp-class.html

Entry: QCStats-class
Aliases: QCStats-class avbg,QCStats-method maxbg,QCStats-method minbg,QCStats-method percent.present,QCStats-method sfs,QCStats-method target,QCStats-method spikeInProbes,QCStats-method qcProbes,QCStats-method ratios,QCStats-method arrayType,QCStats-method avbg-method maxbg-method minbg-method percent.present-method sfs-method target-method spikeInProbes-method qcProbes-method ratios-method arrayType-method avbg maxbg minbg percent.present sfs target spikeInProbes qcProbes ratios arrayType plot,QCStats,ANY-method
Keywords: classes
Description: Class "QCStats"
URL: ../../../library/simpleaffy/html/QCStats-class.html

Entry: all.present
Aliases: all.present
Keywords: misc
Description: Filter by PMA call
URL: ../../../library/simpleaffy/html/all.present.html

Entry: all.present.in.group
Aliases: all.present.in.group
Keywords: misc
Description: Filter by PMA call
URL: ../../../library/simpleaffy/html/all.present.in.group.html

Entry: bg.correct.sa
Aliases: bg.correct.sa
Keywords: misc
Description: Simpleaffy Implementation of Mas5 Background Correction
URL: ../../../library/simpleaffy/html/bg.correct.sa.html

Entry: call.exprs
Aliases: call.exprs
Keywords: misc
Description: Generate Expression Summaries for Affymetrix Data
URL: ../../../library/simpleaffy/html/call.exprs.html

Entry: detection.p.val
Aliases: detection.p.val
Keywords: misc
Description: Calculate Detection p-values
URL: ../../../library/simpleaffy/html/detection.p.val.html

Entry: get.annotation
Aliases: get.annotation write.annotation results.summary
Keywords: misc
Description: Get annotation data for a gene list
URL: ../../../library/simpleaffy/html/get.annotation.html

Entry: get.array.indices
Aliases: get.array.indices get.array.indices,AffyBatch-method get.array.indices,exprSet-method
Keywords: misc
Description: find arrays in an AffyBatch object defined by their phenoData
URL: ../../../library/simpleaffy/html/get.array.indices.html

Entry: get.array.subset
Aliases: get.array.subset get.array.subset,AffyBatch-method get.array.subset,ExpressionSet-method
Keywords: misc
Description: Get a subset of arrays from an affybatch object, split by phnotypic data
URL: ../../../library/simpleaffy/html/get.array.subset.html

Entry: get.array.subset.affybatch
Aliases: get.array.subset.affybatch get.array.subset.exprset
Keywords: misc
Description: Get a subset of arrays from an affybatch object, split by phnotypic data
URL: ../../../library/simpleaffy/html/get.array.subset.affy.html

Entry: get.fold.change.and.t.test
Aliases: get.fold.change.and.t.test
Keywords: misc
Description: Compute fold change and t-test statistics between two experimental groups
URL: ../../../library/simpleaffy/html/get.fold.change.and.t.test.html

Entry: blue.white.red.cols
Aliases: blue.white.red.cols red.black.green.cols red.yellow.white.cols
Keywords: misc
Description: Generate colourings for heatmaps
URL: ../../../library/simpleaffy/html/hmap.colors.html

Entry: hmap.eset
Aliases: hmap.eset
Keywords: misc
Description: Draw a heatmap from an AffyBatch object
URL: ../../../library/simpleaffy/html/hmap.eset.html

Entry: hmap.pc
Aliases: hmap.pc
Keywords: misc
Description: Draw a heatmap from an PairComp object
URL: ../../../library/simpleaffy/html/hmap.pc.html

Entry: journalpng
Aliases: journalpng screenpng
Keywords: misc
Description: Produce a device for producing artwork for presentations and journals
URL: ../../../library/simpleaffy/html/journalpng.html

Entry: justMAS
Aliases: justMAS
Keywords: misc
Description: Generate Expression calls using a C implementation of the MAS 5.0 Algorithm
URL: ../../../library/simpleaffy/html/justMAS.html

Entry: pairwise.comparison
Aliases: pairwise.comparison
Keywords: misc
Description: Compute pairwise comparison statistics between two experimental groups
URL: ../../../library/simpleaffy/html/pairwise.comparison.html

Entry: pairwise.filter
Aliases: pairwise.filter
Keywords: misc
Description: Filter pairwise comparison statistics between two experimental groups
URL: ../../../library/simpleaffy/html/pairwise.filter.html

Entry: plot.pairwise.comparison
Aliases: plot.pairwise.comparison plot,PairComp plot,PairComp-method
Keywords: misc
Description: Plots a PairComp object
URL: ../../../library/simpleaffy/html/plot.pairwise.comparison.html

Entry: plot.qc.stats
Aliases: plot.qc.stats plot,QCStats plot,QCStats,missing-method
Keywords: misc
Description: Plots a QCStats object
URL: ../../../library/simpleaffy/html/plot.qc.stats.html

Entry: qc
Aliases: qc qc,AffyBatch-method
Keywords: misc
Description: Generate QC stats from an AffyBatch object
URL: ../../../library/simpleaffy/html/qc.html

Entry: qc.affy
Aliases: qc.affy
Keywords: misc
Description: Generate Affymetrix Style QC Statistics
URL: ../../../library/simpleaffy/html/qc.affy.html

Entry:  qc.get.alpha1
Aliases: qc.get.alpha1 qc.set.alpha1 qc.get.alpha2 qc.set.alpha2 qc.get.tau
Keywords: misc
Description: Get or set the alpha values for the current QC environment
URL: ../../../library/simpleaffy/html/qc.get.alpha1.html

Entry:  qc.get.array
Aliases: qc.get.array qc.set.array
Keywords: misc
Description: Get or set the name of the array for which the current QC environment is valid. Currently not used for anything important; is a free text identifier.
URL: ../../../library/simpleaffy/html/qc.get.array.html

Entry:  qc.get.probes
Aliases: qc.get.probes qc.get.probe qc.add.probe
Keywords: misc
Description: Retrieve QC probeset names for the current array type
URL: ../../../library/simpleaffy/html/qc.get.probes.html

Entry:  qc.get.ratios
Aliases: qc.get.ratios qc.get.ratio qc.add.ratio
Keywords: misc
Description: Retrieve pairs of probesets used for calculating 3'/5' ratios
URL: ../../../library/simpleaffy/html/qc.get.ratios.html

Entry:  qc.get.spikes
Aliases: qc.get.spikes qc.get.spike qc.add.spike
Keywords: misc
Description: Retrieve QC spike probeset names for the current array type
URL: ../../../library/simpleaffy/html/qc.get.spikes.html

Entry:  qc.have.params 
Aliases: qc.have.params
Keywords: misc
Description: Does simpleaffy have a QC definition file for the specified array?
URL: ../../../library/simpleaffy/html/qc.have.params.html

Entry:  qc.ok 
Aliases: qc.ok
Keywords: misc
Description: Has simpleaffy's QC environment been set up?
URL: ../../../library/simpleaffy/html/qc.ok.html

Entry:  qc.read.file 
Aliases: qc.read.file
Keywords: misc
Description: Read a file defining the QC parameters for a specified array and set up the QC Environment
URL: ../../../library/simpleaffy/html/qc.read.file.html

Entry: qcs
Aliases: qcs
Keywords: datasets
Description: an example QC Stats object
URL: ../../../library/simpleaffy/html/qc.stats.html

Entry: read.affy
Aliases: read.affy
Keywords: misc
Description: Read a Set of .CEL Files and Phenotypic Data
URL: ../../../library/simpleaffy/html/read.affy.html

Entry: read.affy.mixed
Aliases: read.affy.mixed
Keywords: misc
Description: Read a Set of .CEL Files and Phenotypic Data from mixed chip types
URL: ../../../library/simpleaffy/html/read.affy.mixed.html

Entry: setQCEnvironment
Aliases: setQCEnvironment
Keywords: misc
Description: Establish the appropriate QC environment for the specified array
URL: ../../../library/simpleaffy/html/setQCEnvironment.html

Entry:  simpleaffy-deprecated 
Aliases: simpleaffy-deprecated getTao getAlpha1 getAlpha2 getActin3 getActinM getActin5 getGapdh3 getGapdhM getGapdh5 getAllQCProbes getBioB getBioC getBioD getCreX getAllSpikeProbes haveQCParams
Keywords: misc
Description: Does simpleaffy have a QC definition file for the specified array?
URL: ../../../library/simpleaffy/html/simpleaffy-deprecated.html

Entry: standard.pearson
Aliases: standard.pearson
Keywords: misc
Description: A clustering function based on pearson correlation
URL: ../../../library/simpleaffy/html/standard.pearson.html

Entry: trad.scatter.plot
Aliases: trad.scatter.plot
Keywords: misc
Description: Does a Traditional Scatter Plot of Expression Data
URL: ../../../library/simpleaffy/html/trad.scatter.plot.html