A B C D F G H J M P Q R S T W misc
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" |
bg.correct.sa | Simpleaffy Implementation of Mas5 Background Correction |
blue.white.red.cols | Generate colourings for heatmaps |
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 |
detection.p.val | Calculate Detection P Values |
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 |
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 |
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 |
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 |
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" |
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 |
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" |
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 |
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 |
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 |
write.annotation | Get annotation data for a gene list |
[,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 |