Man pages for simpleaffy
Very simple high level analysis of Affymetrix data
| all.present | Filter by PMA call |
| all.present.in.group | Filter by PMA call |
| bg.correct.sa | Simpleaffy Implementation of Mas5 Background Correction |
| call.exprs | Generate Expression Summaries for Affymetrix Data |
| detection.p.val | Calculate Detection p-values |
| get.annotation | Get annotation data for a gene list |
| get.array.indices | Find arrays in an AffyBatch object defined by their phenoData |
| get.array.subset | Get a subset of arrays from an affybatch object, split by... |
| get.array.subset.affy | Get a subset of arrays from an affybatch object, split by... |
| get.fold.change.and.t.test | Compute fold change and t-test statistics between two... |
| hmap.colors | Generate colourings for heatmaps |
| 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... |
| justMAS | Generate Expression calls using a C implementation of the MAS... |
| PairComp-class | Class "PairComp" Represents the results of pairwise... |
| pairwise.comparison | Compute pairwise comparison statistics between two... |
| pairwise.filter | Filter pairwise comparison statistics between two... |
| plot.pairwise.comparison | Plots a PairComp object |
| plot.qc.stats | Plots a QCStats object |
| qc | Generate QC stats from an AffyBatch object |
| qc.affy | Generate Affymetrix Style QC Statistics |
| qc.get.alpha1 | 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... |
| qc.get.probes | Retrieve QC probeset names for the current array type |
| qc.get.ratios | Retrieve pairs of probesets used for calculating 3'/5' ratios |
| qc.get.spikes | Retrieve QC spike probeset names for the current array type |
| qc.have.params | Does simpleaffy have a QC definition file for the specified... |
| qc.ok | Has simpleaffy's QC environment been set up? |
| qc.read.file | Read a file defining the QC parameters for a specified array... |
| qc.stats | an example QC Stats object |
| QCStats-class | 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... |
| setQCEnvironment | Establish the appropriate QC environment for the specified... |
| simpleaffy-deprecated | Does simpleaffy have a QC definition file for the specified... |
| standard.pearson | A clustering function based on pearson correlation |
| trad.scatter.plot | Does a Traditional Scatter Plot of Expression Data |
