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A B C D F G H J M P Q R S T W misc
| all.present | Filter by PMA call |
| all.present.in.group | Filter by PMA call |
| alpha | The alpha paramaters used to calculate PMA calls |
| avbg | Accessor Methods for QCStats class |
| avbg,QCStats-method | Class "QCStats" |
| avbg-methods | Class "QCStats" |
| bg.correct.sa | Simpleaffy Implementation of Mas5 Background Correction |
| blue.white.red.cols | Generate colourings for heatmaps |
| calculated.from | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| calculated.from,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| call.exprs | Generate Expression Summaries for Affymetrix Data |
| calls | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| calls,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| detection.p.val | Calculate Detection P Values |
| fc | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| fc,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| get.annotation | Get annotation data for a gene list |
| get.array.subset | Get a subset of arrays from an affybatch object, split by phnotypic data |
| get.array.subset,AffyBatch-method | Get a subset of arrays from an affybatch object, split by phnotypic data |
| get.array.subset,exprSet-method | Get a subset of arrays from an affybatch object, split by phnotypic data |
| get.array.subset.affybatch | Get a subset of arrays from an affybatch object, split by phnotypic data |
| get.array.subset.exprset | Get a subset of arrays from an affybatch object, split by phnotypic data |
| get.fold.change.and.t.test | Compute fold change and t-test statistics between two experimental groups |
| getActin3 | Gets the probesetid for the specified control probe |
| getActin5 | Gets the probesetid for the specified control probe |
| getActinM | Gets the probesetid for the specified control probe |
| getAllQCProbes | Get the names of all the QC (not spike-in) probes on the array |
| getAllSpikeProbes | Get the names of all the Spike (not QC) probes on the array |
| getAlpha1 | Gets the probesetid for the specified control probe |
| getAlpha2 | Gets the probesetid for the specified control probe |
| getBioB | Gets the probesetid for the specified control probe |
| getBioC | Gets the probesetid for the specified control probe |
| getBioD | Gets the probesetid for the specified control probe |
| getCreX | Gets the probesetid for the specified control probe |
| getGapdh3 | Gets the probesetid for the specified control probe |
| getGapdh5 | Gets the probesetid for the specified control probe |
| getGapdhM | Gets the probesetid for the specified control probe |
| getQCParams | Get Array Dependent QC Parameters |
| getQCParams,AffyBatch-method | Get Array Dependent QC Parameters |
| getQCParams-methods | Get Array Dependent QC Parameters |
| getTao | Gets the probesetid for the specified control probe |
| group | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| group,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| haveQCParams | True if data exists in the QC environment describing the specified chip |
| hmap.eset | Draw a heatmap from an AffyBatch object |
| hmap.pc | Draw a heatmap from an PairComp object |
| journalpng | Produce a device for producing artwork for presentations and journals |
| justMAS | Generate Expression calls using a C implementation of the MAS 5.0 Algorithm |
| maxbg | Accessor Methods for QCStats class |
| maxbg,QCStats-method | Class "QCStats" |
| maxbg-methods | Class "QCStats" |
| means | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| means,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| members | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| members,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| minbg | Accessor Methods for QCStats class |
| minbg,QCStats-method | Class "QCStats" |
| minbg-methods | Class "QCStats" |
| PairComp-class | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| pairwise.comparison | Compute pairwise comparison statistics between two experimental groups |
| pairwise.filter | Filter pairwise comparison statistics between two experimental groups |
| pairwise.filter,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| pData | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| pData,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| percent.present | Accessor Methods for QCStats class |
| percent.present,QCStats-method | Class "QCStats" |
| percent.present-methods | Class "QCStats" |
| plot,PairComp | Plots a PairComp object |
| plot,PairComp-method | Plots a PairComp object |
| plot,QCStats | Plots a QCStats object |
| plot,QCStats-method | Plots a QCStats object |
| plot.pairwise.comparison | Plots a PairComp object |
| plot.qc.stats | Plots a QCStats object |
| plot.qc.stats2 | Plots a QCStats object |
| qc | Generate QC stats from an AffyBatch object |
| qc,AffyBatch-method | Generate QC stats from an AffyBatch object |
| qc.affy | Generate Affymetrix Style QC Statistics |
| qc.probes | The name of the QC probes |
| qcProbes | Accessor Methods for QCStats class |
| qcProbes,QCStats-method | Class "QCStats" |
| qcProbes-methods | Class "QCStats" |
| QCStats-class | Class "QCStats" |
| ratios | Accessor Methods for QCStats class |
| ratios,QCStats-method | Class "QCStats" |
| ratios-methods | Class "QCStats" |
| read.affy | Read a Set of .CEL Files and Phenotypic Data |
| read.affy.mixed | Read a Set of .CEL Files and Phenotypic Data from mixed chip types |
| red.black.green.cols | Generate colourings for heatmaps |
| red.yellow.white.cols | Generate colourings for heatmaps |
| results.summary | Get annotation data for a gene list |
| screenpng | Produce a device for producing artwork for presentations and journals |
| sfs | Accessor Methods for QCStats class |
| sfs,QCStats-method | Class "QCStats" |
| sfs-methods | Class "QCStats" |
| spikeInProbes | Accessor Methods for QCStats class |
| spikeInProbes,QCStats-method | Class "QCStats" |
| spikeInProbes-methods | Class "QCStats" |
| spikes | The name of the spike probes |
| standard.pearson | A clustering function based on pearson correlation |
| target | Accessor Methods for QCStats class |
| target,QCStats-method | Class "QCStats" |
| target-methods | Class "QCStats" |
| trad.scatter.plot | Does a Traditional Scatter Plot of Expression Data |
| tt | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| tt,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| write.annotation | Get annotation data for a gene list |
| [,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| [<-,PairComp-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |