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

Entry: bioB
Aliases: bioB bioC bioD actin3 actin35 actin3M actin5 actinM avbg creX gapdh3 gapdh35 gapdh5 gapdhM gapdh3M maxbg minbg percent.present sfs target
Keywords: misc 
Description: Accessor Methods for QCStats class
URL: ../../../library/simpleaffy/html/QCStats-accessor.html

Entry: QCStats-class
Aliases: QCStats-class actin35,QCStats-method actin3,QCStats-method actin3M,QCStats-method actin5,QCStats-method actinM,QCStats-method avbg,QCStats-method bioB,QCStats-method bioC,QCStats-method bioD,QCStats-method creX,QCStats-method gapdh35,QCStats-method gapdh3,QCStats-method gapdh3M,QCStats-method gapdh5,QCStats-method gapdhM,QCStats-method maxbg,QCStats-method minbg,QCStats-method percent.present,QCStats-method sfs,QCStats-method target,QCStats-method actin35-methods actin3-methods actin3M-methods actin5-methods actinM-methods avbg-methods bioB-methods bioC-methods bioD-methods creX-methods gapdh35-methods gapdh3-methods gapdh3M-methods gapdh5-methods gapdhM-methods maxbg-methods minbg-methods percent.present-methods sfs-methods target-methods
Keywords: classes
Description: Class "QCStats"
URL: ../../../library/simpleaffy/html/QCStats-class.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.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: 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: 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.qc.stats
Aliases: plot.qc.stats 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: 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: 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
