Man pages for simpleaffy
Very simple high level analysis of Affymetrix data

all.presentFilter by PMA call
all.present.in.groupFilter by PMA call
bg.correct.saSimpleaffy Implementation of Mas5 Background Correction
call.exprsGenerate Expression Summaries for Affymetrix Data
detection.p.valCalculate Detection p-values
get.annotationGet annotation data for a gene list
get.array.indicesFind arrays in an AffyBatch object defined by their phenoData
get.array.subsetGet a subset of arrays from an affybatch object, split by...
get.array.subset.affyGet a subset of arrays from an affybatch object, split by...
get.fold.change.and.t.testCompute fold change and t-test statistics between two...
hmap.colorsGenerate colourings for heatmaps
hmap.esetDraw a heatmap from an AffyBatch object
hmap.pcDraw a heatmap from an PairComp object
journalpngProduce a device for producing artwork for presentations and...
justMASGenerate Expression calls using a C implementation of the MAS...
PairComp-classClass "PairComp" Represents the results of pairwise...
pairwise.comparisonCompute pairwise comparison statistics between two...
pairwise.filterFilter pairwise comparison statistics between two...
plot.pairwise.comparisonPlots a PairComp object
plot.qc.statsPlots a QCStats object
qcGenerate QC stats from an AffyBatch object
qc.affyGenerate Affymetrix Style QC Statistics
qc.get.alpha1Get or set the alpha values for the current QC environment
qc.get.arrayGet or set the name of the array for which the current QC...
qc.get.probesRetrieve QC probeset names for the current array type
qc.get.ratiosRetrieve pairs of probesets used for calculating 3'/5' ratios
qc.get.spikesRetrieve QC spike probeset names for the current array type
qc.have.paramsDoes simpleaffy have a QC definition file for the specified...
qc.okHas simpleaffy's QC environment been set up?
qc.read.fileRead a file defining the QC parameters for a specified array...
qc.statsan example QC Stats object
QCStats-classClass "QCStats"
read.affyRead a Set of .CEL Files and Phenotypic Data
read.affy.mixedRead a Set of .CEL Files and Phenotypic Data from mixed chip...
setQCEnvironmentEstablish the appropriate QC environment for the specified...
simpleaffy-deprecatedDoes simpleaffy have a QC definition file for the specified...
standard.pearsonA clustering function based on pearson correlation
trad.scatter.plotDoes a Traditional Scatter Plot of Expression Data
simpleaffy documentation built on Nov. 17, 2017, 12:22 p.m.