![[R logo]](../../../doc/html/Rlogo.svg)
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
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 |
| arrayType | Class "QCStats" |
| arrayType-method | Class "QCStats" |
| avbg | Class "QCStats" |
| avbg-method | 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-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-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-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| get.annotation | Get annotation data for a gene list |
| get.array.indices | Find arrays in an AffyBatch object defined by their phenoData |
| get.array.indices-method | Find arrays in an AffyBatch object defined by their phenoData |
| get.array.subset | Get a subset of arrays from an affybatch object, split by phnotypic data |
| get.array.subset-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 | Does simpleaffy have a QC definition file for the specified array? |
| getActin5 | Does simpleaffy have a QC definition file for the specified array? |
| getActinM | Does simpleaffy have a QC definition file for the specified array? |
| getAllQCProbes | Does simpleaffy have a QC definition file for the specified array? |
| getAllSpikeProbes | Does simpleaffy have a QC definition file for the specified array? |
| getAlpha1 | Does simpleaffy have a QC definition file for the specified array? |
| getAlpha2 | Does simpleaffy have a QC definition file for the specified array? |
| getBioB | Does simpleaffy have a QC definition file for the specified array? |
| getBioC | Does simpleaffy have a QC definition file for the specified array? |
| getBioD | Does simpleaffy have a QC definition file for the specified array? |
| getCreX | Does simpleaffy have a QC definition file for the specified array? |
| getGapdh3 | Does simpleaffy have a QC definition file for the specified array? |
| getGapdh5 | Does simpleaffy have a QC definition file for the specified array? |
| getGapdhM | Does simpleaffy have a QC definition file for the specified array? |
| getTao | Does simpleaffy have a QC definition file for the specified array? |
| group | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| group-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| haveQCParams | Does simpleaffy have a QC definition file for the specified array? |
| 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 | Class "QCStats" |
| maxbg-method | Class "QCStats" |
| means | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| means-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-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| minbg | Class "QCStats" |
| minbg-method | 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-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-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| percent.present | Class "QCStats" |
| percent.present-method | Class "QCStats" |
| plot,PairComp | Plots a PairComp object |
| plot,QCStats | Plots a QCStats object |
| plot-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| plot-method | Class "QCStats" |
| plot-method | Plots a PairComp object |
| plot-method | Plots a QCStats object |
| plot.pairwise.comparison | Plots a PairComp object |
| plot.qc.stats | Plots a QCStats object |
| qc | Generate QC stats from an AffyBatch object |
| qc-method | Generate QC stats from an AffyBatch object |
| qc.add.probe | Retrieve QC probeset names for the current array type |
| qc.add.ratio | Retrieve pairs of probesets used for calculating 3'/5' ratios |
| qc.add.spike | Retrieve QC spike probeset names for the current array type |
| qc.affy | Generate Affymetrix Style QC Statistics |
| qc.get.alpha1 | Get or set the alpha values for the current QC environment |
| qc.get.alpha2 | Get or set the alpha values for the current QC environment |
| qc.get.array | 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. |
| qc.get.probe | Retrieve QC probeset names for the current array type |
| qc.get.probes | Retrieve QC probeset names for the current array type |
| qc.get.ratio | Retrieve pairs of probesets used for calculating 3'/5' ratios |
| qc.get.ratios | Retrieve pairs of probesets used for calculating 3'/5' ratios |
| qc.get.spike | Retrieve QC spike probeset names for the current array type |
| qc.get.spikes | Retrieve QC spike probeset names for the current array type |
| qc.get.tau | Get or set the alpha values for the current QC environment |
| qc.have.params | Does simpleaffy have a QC definition file for the specified array? |
| qc.ok | Has simpleaffy's QC environment been set up? |
| qc.read.file | Read a file defining the QC parameters for a specified array and set up the QC Environment |
| qc.set.alpha1 | Get or set the alpha values for the current QC environment |
| qc.set.alpha2 | Get or set the alpha values for the current QC environment |
| qc.set.array | 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. |
| qcProbes | Class "QCStats" |
| qcProbes-method | Class "QCStats" |
| qcs | an example QC Stats object |
| QCStats-class | Class "QCStats" |
| ratios | Class "QCStats" |
| ratios-method | 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 |
| setQCEnvironment | Establish the appropriate QC environment for the specified array |
| sfs | Class "QCStats" |
| sfs-method | Class "QCStats" |
| simpleaffy-deprecated | Does simpleaffy have a QC definition file for the specified array? |
| spikeInProbes | Class "QCStats" |
| spikeInProbes-method | Class "QCStats" |
| standard.pearson | A clustering function based on pearson correlation |
| target | Class "QCStats" |
| target-method | 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-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| write.annotation | Get annotation data for a gene list |
| [-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| [<--method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors |