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
Keywords: classes
Description: Class "PairComp" Represents the results of pairwise comparison between two experimental factors
URL: ../../../library/simpleaffy/html/PairComp-class.html

Entry: spikeInProbes
Aliases: spikeInProbes qcProbes avbg maxbg minbg percent.present sfs target ratios
Keywords: misc
Description: Accessor Methods for QCStats class
URL: ../../../library/simpleaffy/html/QCStats-accessor.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 avbg-methods maxbg-methods minbg-methods percent.present-methods sfs-methods target-methods spikeInProbes-methods qcProbes-methods ratios-methods
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: alpha
Aliases: alpha
Keywords: datasets
Description: The alpha paramaters used to calculate PMA calls
URL: ../../../library/simpleaffy/html/alpha.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,exprSet-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: getActin3
Aliases: getActin3
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getActin3.html

Entry: getActin5
Aliases: getActin5
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getActin5.html

Entry: getActinM
Aliases: getActinM
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getActinM.html

Entry: getAllQCProbes
Aliases: getAllQCProbes
Keywords: misc
Description: Get the names of all the QC (not spike-in) probes on the array
URL: ../../../library/simpleaffy/html/getAllQCProbes.html

Entry: getAllSpikeProbes
Aliases: getAllSpikeProbes
Keywords: misc
Description: Get the names of all the Spike (not QC) probes on the array
URL: ../../../library/simpleaffy/html/getAllSpikeProbes.html

Entry: getAlpha1
Aliases: getAlpha1
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getAlpha1.html

Entry: getTao
Aliases: getTao
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getAlpha2.html

Entry: getBioB
Aliases: getBioB
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getBioB.html

Entry: getBioC
Aliases: getBioC
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getBioC.html

Entry: getBioD
Aliases: getBioD
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getBioD.html

Entry: getCreX
Aliases: getCreX
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getCreX.html

Entry: getGapdh3
Aliases: getGapdh3
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getGapdh3.html

Entry: getGapdh5
Aliases: getGapdh5
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getGapdh5.html

Entry: getGapdhM
Aliases: getGapdhM
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getGapdhM.html

Entry: getQCParams-methods
Aliases: getQCParams-methods getQCParams,AffyBatch-method getQCParams
Keywords: methods
Description: Get Array Dependent QC Parameters
URL: ../../../library/simpleaffy/html/getQCParams-methods.html

Entry: getAlpha2
Aliases: getAlpha2
Keywords: misc
Description: Gets the probesetid for the specified control probe
URL: ../../../library/simpleaffy/html/getTao.html

Entry: haveQCParams
Aliases: haveQCParams
Keywords: misc
Description: True if data exists in the QC environment describing the specified chip
URL: ../../../library/simpleaffy/html/haveQCParams.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.qc.stats2 plot,QCStats plot,QCStats-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.probes
Aliases: qc.probes
Keywords: datasets
Description: The name of the QC probes
URL: ../../../library/simpleaffy/html/qc.probes.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: spikes
Aliases: spikes
Keywords: datasets
Description: The name of the spike probes
URL: ../../../library/simpleaffy/html/spikes.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
