Reference index for {aroma.affymetrix}
You are viewing package members beginning with the letter "A"
| Function/Class | Description |
|---|---|
| AffymetrixCelFile.plotMvsA {aroma.affymetrix} | Plots log-ratio versus log-intensity in a scatter plot |
| AffymetrixCelFile.plotMvsX {aroma.affymetrix} | Plots log-ratio versus another variable in a scatter plot |
| AffymetrixCelFile.readRawData {aroma.affymetrix} | Gets all or a subset of the fields in a CEL file |
| AffymetrixCelFile.readUnits {aroma.affymetrix} | Reads CEL data unit by unit |
| AffymetrixCelFile.setCdf {aroma.affymetrix} | Sets the CDF structure for this CEL file |
| AffymetrixCelFile.smoothScatterMvsA {aroma.affymetrix} | Plots log-ratio versus log-intensity in a smooth scatter plot |
| AffymetrixCelFile.updateUnits {aroma.affymetrix} | Updates CEL data unit by unit |
| AffymetrixCelFile.writeImage {aroma.affymetrix} | Writes a spatial image of the signals in the CEL file |
| AffymetrixCelSet {aroma.affymetrix} | The AffymetrixCelSet class |
| AffymetrixCelSet.bgAdjustGcrma {aroma.affymetrix} | Applies probe sequence based background correction to a set of CEL files |
| AffymetrixCelSet.bgAdjustOptical {aroma.affymetrix} | Applies optical background correction to a set of CEL files |
| AffymetrixCelSet.bgAdjustRma {aroma.affymetrix} | Applies RMA background correction to a set of CEL files |
| AffymetrixCelSet.calculateParametersGsb {aroma.affymetrix} | Computes parameters for adjustment of specific binding |
| AffymetrixCelSet.doFIRMA {aroma.affymetrix} | Finding Isoforms using Robust Multichip Analysis (FIRMA) |
| AffymetrixCelSet.extractAffyBatch {aroma.affymetrix} | Extracts an in-memory AffyBatch object from the CEL set |
| AffymetrixCelSet.extractFeatureSet {aroma.affymetrix} | Extracts CEL signals an in-memory FeatureSet object |
| AffymetrixCelSet.extractMatrix {aroma.affymetrix} | Extract data as a matrix for a set of arrays |
| AffymetrixCelSet.getAverageFile {aroma.affymetrix} | Calculates the mean and the standard deviation of the cell signal (intensity, standard deviation etc.) across the CEL set |
| AffymetrixCelSet.getCdf {aroma.affymetrix} | Gets the CDF structure for this CEL set |
| AffymetrixCelSet.getChipType {aroma.affymetrix} | Gets the chip type for this CEL set |