# Very simple high level analysis of Affymetrix data

## Documentation for package ‘simpleaffy’ version 2.52.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D F G H J M P Q R S T W misc

## -- A --

all.present | Filter by PMA call
all.present.in.group | Filter by PMA call
arrayType | Class "QCStats"
arrayType-method | Class "QCStats"
avbg | Class "QCStats"
avbg-method | Class "QCStats"

## -- B --

bg.correct.sa | Simpleaffy Implementation of Mas5 Background Correction
blue.white.red.cols | Generate colourings for heatmaps

## -- C --

calculated.from | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
calculated.from-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
call.exprs | Generate Expression Summaries for Affymetrix Data
calls | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
calls-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors

## -- D --

detection.p.val | Calculate Detection p-values

## -- F --

fc | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
fc-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors

## -- G --

get.annotation | Get annotation data for a gene list
get.array.indices | Find arrays in an AffyBatch object defined by their phenoData
get.array.indices-method | Find arrays in an AffyBatch object defined by their phenoData
get.array.subset | Get a subset of arrays from an affybatch object, split by phnotypic data
get.array.subset-method | Get a subset of arrays from an affybatch object, split by phnotypic data
get.array.subset.affybatch | Get a subset of arrays from an affybatch object, split by phnotypic data
get.array.subset.exprset | Get a subset of arrays from an affybatch object, split by phnotypic data
get.fold.change.and.t.test | Compute fold change and t-test statistics between two experimental groups
getActin3 | Does simpleaffy have a QC definition file for the specified array?
getActin5 | Does simpleaffy have a QC definition file for the specified array?
getActinM | Does simpleaffy have a QC definition file for the specified array?
getAllQCProbes | Does simpleaffy have a QC definition file for the specified array?
getAllSpikeProbes | Does simpleaffy have a QC definition file for the specified array?
getAlpha1 | Does simpleaffy have a QC definition file for the specified array?
getAlpha2 | Does simpleaffy have a QC definition file for the specified array?
getBioB | Does simpleaffy have a QC definition file for the specified array?
getBioC | Does simpleaffy have a QC definition file for the specified array?
getBioD | Does simpleaffy have a QC definition file for the specified array?
getCreX | Does simpleaffy have a QC definition file for the specified array?
getGapdh3 | Does simpleaffy have a QC definition file for the specified array?
getGapdh5 | Does simpleaffy have a QC definition file for the specified array?
getGapdhM | Does simpleaffy have a QC definition file for the specified array?
getTao | Does simpleaffy have a QC definition file for the specified array?
group | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
group-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors

## -- H --

haveQCParams | Does simpleaffy have a QC definition file for the specified array?
hmap.eset | Draw a heatmap from an AffyBatch object
hmap.pc | Draw a heatmap from an PairComp object

## -- J --

journalpng | Produce a device for producing artwork for presentations and journals
justMAS | Generate Expression calls using a C implementation of the MAS 5.0 Algorithm

## -- M --

maxbg | Class "QCStats"
maxbg-method | Class "QCStats"
means | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
means-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
members | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
members-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
minbg | Class "QCStats"
minbg-method | Class "QCStats"

## -- P --

PairComp-class | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
pairwise.comparison | Compute pairwise comparison statistics between two experimental groups
pairwise.filter | Filter pairwise comparison statistics between two experimental groups
pairwise.filter-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
pData | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
pData-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
percent.present | Class "QCStats"
percent.present-method | Class "QCStats"
plot,PairComp | Plots a PairComp object
plot,QCStats | Plots a QCStats object
plot-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
plot-method | Class "QCStats"
plot-method | Plots a PairComp object
plot-method | Plots a QCStats object
plot.pairwise.comparison | Plots a PairComp object
plot.qc.stats | Plots a QCStats object

## -- Q --

qc | Generate QC stats from an AffyBatch object
qc-method | Generate QC stats from an AffyBatch object
qc.add.probe | Retrieve QC probeset names for the current array type
qc.add.ratio | Retrieve pairs of probesets used for calculating 3'/5' ratios
qc.add.spike | Retrieve QC spike probeset names for the current array type
qc.affy | Generate Affymetrix Style QC Statistics
qc.get.alpha1 | Get or set the alpha values for the current QC environment
qc.get.alpha2 | 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 environment is valid. Currently not used for anything important; is a free text identifier.
qc.get.probe | Retrieve QC probeset names for the current array type
qc.get.probes | Retrieve QC probeset names for the current array type
qc.get.ratio | Retrieve pairs of probesets used for calculating 3'/5' ratios
qc.get.ratios | Retrieve pairs of probesets used for calculating 3'/5' ratios
qc.get.spike | Retrieve QC spike probeset names for the current array type
qc.get.spikes | Retrieve QC spike probeset names for the current array type
qc.get.tau | Get or set the alpha values for the current QC environment
qc.have.params | Does simpleaffy have a QC definition file for the specified array?
qc.ok | Has simpleaffy's QC environment been set up?
qc.read.file | Read a file defining the QC parameters for a specified array and set up the QC Environment
qc.set.alpha1 | Get or set the alpha values for the current QC environment
qc.set.alpha2 | Get or set the alpha values for the current QC environment
qc.set.array | 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.
qcProbes | Class "QCStats"
qcProbes-method | Class "QCStats"
qcs | an example QC Stats object
QCStats-class | Class "QCStats"

## -- R --

ratios | Class "QCStats"
ratios-method | 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 types
red.black.green.cols | Generate colourings for heatmaps
red.yellow.white.cols | Generate colourings for heatmaps
results.summary | Get annotation data for a gene list

## -- S --

screenpng | Produce a device for producing artwork for presentations and journals
setQCEnvironment | Establish the appropriate QC environment for the specified array
sfs | Class "QCStats"
sfs-method | Class "QCStats"
simpleaffy-deprecated | Does simpleaffy have a QC definition file for the specified array?
spikeInProbes | Class "QCStats"
spikeInProbes-method | Class "QCStats"
standard.pearson | A clustering function based on pearson correlation

## -- T --

target | Class "QCStats"
target-method | Class "QCStats"
trad.scatter.plot | Does a Traditional Scatter Plot of Expression Data
tt | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
tt-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors

## -- W --

write.annotation | Get annotation data for a gene list

## -- misc --

[-method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors
[<--method | Class "PairComp" Represents the results of pairwise comparison between two experimental factors