Class "PairComp" Represents the results of pairwise comparison between two experimental factors
Class "QCStats"
Filter by PMA call
Filter by PMA call
Simpleaffy Implementation of Mas5 Background Correction
Generate Expression Summaries for Affymetrix Data
Calculate Detection p-values
Get annotation data for a gene list
Find arrays in an AffyBatch object defined by their phenoData
Get a subset of arrays from an affybatch object, split by phnotypic data
Get a subset of arrays from an affybatch object, split by phnotypic data
Compute fold change and t-test statistics between two experimental groups
Generate colourings for heatmaps
Draw a heatmap from an AffyBatch object
Draw a heatmap from an PairComp object
Produce a device for producing artwork for presentations and journals
Generate Expression calls using a C implementation of the MAS 5.0 Algorithm
Compute pairwise comparison statistics between two experimental groups
Filter pairwise comparison statistics between two experimental groups
Plots a PairComp object
Plots a QCStats object
Generate QC stats from an AffyBatch object
Generate Affymetrix Style QC Statistics
Get or set the alpha values for the current QC environment
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.
Retrieve QC probeset names for the current array type
Retrieve pairs of probesets used for calculating 3'/5' ratios
Retrieve QC spike probeset names for the current array type
Does simpleaffy have a QC definition file for the specified array?
Has simpleaffy's QC environment been set up?
Read a file defining the QC parameters for a specified array and set up the QC Environment
an example QC Stats object
Read a Set of .CEL Files and Phenotypic Data
Read a Set of .CEL Files and Phenotypic Data from mixed chip types
Establish the appropriate QC environment for the specified array
Does simpleaffy have a QC definition file for the specified array?
A clustering function based on pearson correlation
Does a Traditional Scatter Plot of Expression Data