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,AffyBatch-method |
Find arrays in an AffyBatch object defined by their phenoData |
get.array.indices,ExpressionSet-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,AffyBatch-method |
Get a subset of arrays from an affybatch object, split by phnotypic data |
get.array.subset,ExpressionSet-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,PairComp-method |
Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
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 |
Class "QCStats" |
percent.present,QCStats-method |
Class "QCStats" |
percent.present-method |
Class "QCStats" |
plot,PairComp |
Plots a PairComp object |
plot,PairComp,ANY-method |
Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
plot,PairComp,missing-method |
Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
plot,PairComp,PairComp-method |
Class "PairComp" Represents the results of pairwise comparison between two experimental factors |
plot,PairComp-method |
Plots a PairComp object |
plot,QCStats |
Plots a QCStats object |
plot,QCStats,ANY-method |
Class "QCStats" |
plot,QCStats,missing-method |
Plots a QCStats object |
plot.pairwise.comparison |
Plots a PairComp object |
plot.qc.stats |
Plots a QCStats object |
qc |
Generate QC stats from an AffyBatch object |
qc,AffyBatch-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,QCStats-method |
Class "QCStats" |
qcProbes-method |
Class "QCStats" |
qcs |
an example QC Stats object |
QCStats-class |
Class "QCStats" |