Very simple high level analysis of Affymetrix data


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Documentation for package `simpleaffy' version 2.0.13

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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
alpha The alpha paramaters used to calculate PMA calls
avbg Accessor Methods for QCStats class
avbg,QCStats-method Class "QCStats"
avbg-methods 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,PairComp-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,PairComp-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,PairComp-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.subset Get a subset of arrays from an affybatch object, split by phnotypic data
get.array.subset,AffyBatch-method Get a subset of arrays from an affybatch object, split by phnotypic data
get.array.subset,exprSet-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 Gets the probesetid for the specified control probe
getActin5 Gets the probesetid for the specified control probe
getActinM Gets the probesetid for the specified control probe
getAllQCProbes Get the names of all the QC (not spike-in) probes on the array
getAllSpikeProbes Get the names of all the Spike (not QC) probes on the array
getAlpha1 Gets the probesetid for the specified control probe
getAlpha2 Gets the probesetid for the specified control probe
getBioB Gets the probesetid for the specified control probe
getBioC Gets the probesetid for the specified control probe
getBioD Gets the probesetid for the specified control probe
getCreX Gets the probesetid for the specified control probe
getGapdh3 Gets the probesetid for the specified control probe
getGapdh5 Gets the probesetid for the specified control probe
getGapdhM Gets the probesetid for the specified control probe
getQCParams Get Array Dependent QC Parameters
getQCParams,AffyBatch-method Get Array Dependent QC Parameters
getQCParams-methods Get Array Dependent QC Parameters
getTao Gets the probesetid for the specified control probe
group Class "PairComp" Represents the results of pairwise comparison between two experimental factors
group,PairComp-method Class "PairComp" Represents the results of pairwise comparison between two experimental factors

-- H --

haveQCParams True if data exists in the QC environment describing the specified chip
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 Accessor Methods for QCStats class
maxbg,QCStats-method Class "QCStats"
maxbg-methods Class "QCStats"
means Class "PairComp" Represents the results of pairwise comparison between two experimental factors
means,PairComp-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,PairComp-method Class "PairComp" Represents the results of pairwise comparison between two experimental factors
minbg Accessor Methods for QCStats class
minbg,QCStats-method Class "QCStats"
minbg-methods 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,PairComp-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,PairComp-method Class "PairComp" Represents the results of pairwise comparison between two experimental factors
percent.present Accessor Methods for QCStats class
percent.present,QCStats-method Class "QCStats"
percent.present-methods Class "QCStats"
plot,PairComp Plots a PairComp object
plot,PairComp-method Plots a PairComp object
plot,QCStats Plots a QCStats object
plot,QCStats-method Plots a QCStats object
plot.pairwise.comparison Plots a PairComp object
plot.qc.stats Plots a QCStats object
plot.qc.stats2 Plots a QCStats object

-- Q --

qc Generate QC stats from an AffyBatch object
qc,AffyBatch-method Generate QC stats from an AffyBatch object
qc.affy Generate Affymetrix Style QC Statistics
qc.probes The name of the QC probes
qcProbes Accessor Methods for QCStats class
qcProbes,QCStats-method Class "QCStats"
qcProbes-methods Class "QCStats"
QCStats-class Class "QCStats"

-- R --

ratios Accessor Methods for QCStats class
ratios,QCStats-method Class "QCStats"
ratios-methods 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
sfs Accessor Methods for QCStats class
sfs,QCStats-method Class "QCStats"
sfs-methods Class "QCStats"
spikeInProbes Accessor Methods for QCStats class
spikeInProbes,QCStats-method Class "QCStats"
spikeInProbes-methods Class "QCStats"
spikes The name of the spike probes
standard.pearson A clustering function based on pearson correlation

-- T --

target Accessor Methods for QCStats class
target,QCStats-method Class "QCStats"
target-methods 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,PairComp-method Class "PairComp" Represents the results of pairwise comparison between two experimental factors

-- W --

write.annotation Get annotation data for a gene list

-- misc --

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