| 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,AffyBatch-method |
Find arrays in an AffyBatch object defined by their phenoData |
| get.array.indices,ExpressionSet-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,AffyBatch-method |
Get a subset of arrays from an affybatch object, split by phnotypic data |
| get.array.subset,ExpressionSet-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,PairComp-method |
Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| 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 |
Class "QCStats" |
| percent.present,QCStats-method |
Class "QCStats" |
| percent.present-method |
Class "QCStats" |
| plot,PairComp |
Plots a PairComp object |
| plot,PairComp,ANY-method |
Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| plot,PairComp,missing-method |
Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| plot,PairComp,PairComp-method |
Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
| plot,PairComp-method |
Plots a PairComp object |
| plot,QCStats |
Plots a QCStats object |
| plot,QCStats,ANY-method |
Class "QCStats" |
| plot,QCStats,missing-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,AffyBatch-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,QCStats-method |
Class "QCStats" |
| qcProbes-method |
Class "QCStats" |
| qcs |
an example QC Stats object |
| QCStats-class |
Class "QCStats" |