Very simple high level analysis of Affymetrix data


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

-- A --

actin3 Accessor Methods for QCStats class
actin3,QCStats-method Class "QCStats"
actin3-methods Class "QCStats"
actin35 Accessor Methods for QCStats class
actin35,QCStats-method Class "QCStats"
actin35-methods Class "QCStats"
actin3M Accessor Methods for QCStats class
actin3M,QCStats-method Class "QCStats"
actin3M-methods Class "QCStats"
actin5 Accessor Methods for QCStats class
actin5,QCStats-method Class "QCStats"
actin5-methods Class "QCStats"
actinM Accessor Methods for QCStats class
actinM,QCStats-method Class "QCStats"
actinM-methods Class "QCStats"
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
bioB Accessor Methods for QCStats class
bioB,QCStats-method Class "QCStats"
bioB-methods Class "QCStats"
bioC Accessor Methods for QCStats class
bioC,QCStats-method Class "QCStats"
bioC-methods Class "QCStats"
bioD Accessor Methods for QCStats class
bioD,QCStats-method Class "QCStats"
bioD-methods Class "QCStats"

-- C --

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
creX Accessor Methods for QCStats class
creX,QCStats-method Class "QCStats"
creX-methods Class "QCStats"

-- 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 --

gapdh3 Accessor Methods for QCStats class
gapdh3,QCStats-method Class "QCStats"
gapdh3-methods Class "QCStats"
gapdh35 Accessor Methods for QCStats class
gapdh35,QCStats-method Class "QCStats"
gapdh35-methods Class "QCStats"
gapdh3M Accessor Methods for QCStats class
gapdh3M,QCStats-method Class "QCStats"
gapdh3M-methods Class "QCStats"
gapdh5 Accessor Methods for QCStats class
gapdh5,QCStats-method Class "QCStats"
gapdh5-methods Class "QCStats"
gapdhM Accessor Methods for QCStats class
gapdhM,QCStats-method Class "QCStats"
gapdhM-methods Class "QCStats"
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
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

-- 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
percent.present Accessor Methods for QCStats class
percent.present,QCStats-method Class "QCStats"
percent.present-methods Class "QCStats"
plot,QCStats Plots a QCStats object
plot,QCStats-method Plots a QCStats object
plot.qc.stats 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
QCStats-class Class "QCStats"

-- R --

read.affy Read a Set of .CEL Files and Phenotypic Data
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"

-- 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