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