A B C D E F G H I L M N P Q R S T U V W X
xps-package | xps Package Overview |
addData | Import additional CEL files into a DataTreeSet |
addData-method | Class DataTreeSet |
addData-methods | Import additional CEL files into a DataTreeSet |
AffyRNAdeg | Functions to assess RNA Degradation. |
AnalysisTreeSet | Class AnalysisTreeSet |
AnalysisTreeSet-class | Class AnalysisTreeSet |
arrayInfo | Class ProjectInfo |
arrayInfo-method | Class ProjectInfo |
arrayInfo<- | Class ProjectInfo |
arrayInfo<--method | Class ProjectInfo |
attachBgrd | Attach/Remove Background Intensities |
attachBgrd-method | Class DataTreeSet |
attachBgrd-methods | Attach/Remove Background Intensities |
attachCall | Attach/Remove Detecion Call Measures |
attachCall-method | Class CallTreeSet |
attachCall-methods | Attach/Remove Detecion Call Measures |
attachData | Attach/Remove Data |
attachData-method | Class ProcesSet |
attachData-methods | Attach/Remove Data |
attachDataXY | Attach/Remove (X,Y)-Coordinates |
attachDataXY-method | Class DataTreeSet |
attachDataXY-methods | Attach/Remove (X,Y)-Coordinates |
attachExpr | Attach/Remove Expression Measures |
attachExpr-method | Class ExprTreeSet |
attachExpr-methods | Attach/Remove Expression Measures |
attachInten | Attach/Remove Intensities |
attachInten-method | Class DataTreeSet |
attachInten-methods | Attach/Remove Intensities |
attachMask | Attach/Remove Scheme Mask |
attachMask-method | Class DataTreeSet |
attachMask-method | Class SchemeTreeSet |
attachMask-methods | Attach/Remove Scheme Mask |
attachProbe | Attach/Remove Probe Sequence and/or GC Content |
attachProbe-method | Class SchemeTreeSet |
attachProbe-methods | Attach/Remove Probe Sequence and/or GC Content |
attachProbeContentGC | Attach/Remove Probe Sequence and/or GC Content |
attachProbeContentGC-method | Class DataTreeSet |
attachProbeContentGC-method | Class SchemeTreeSet |
attachProbeContentGC-methods | Attach/Remove Probe Sequence and/or GC Content |
attachProbeSequence | Attach/Remove Probe Sequence and/or GC Content |
attachProbeSequence-method | Class SchemeTreeSet |
attachPVal | Attach/Remove Detecion Call Measures |
attachPVal-method | Class CallTreeSet |
attachPVal-methods | Attach/Remove Detecion Call Measures |
attachUnitNames | Attach/Remove Unit Names |
attachUnitNames-method | Class DataTreeSet |
attachUnitNames-method | Class SchemeTreeSet |
attachUnitNames-methods | Attach/Remove Unit Names |
authorInfo | Class ProjectInfo |
authorInfo-method | Class ProjectInfo |
authorInfo<- | Class ProjectInfo |
authorInfo<--method | Class ProjectInfo |
background | Class DataTreeSet |
background-method | Class DataTreeSet |
background<- | Class DataTreeSet |
background<--method | Class DataTreeSet |
bgcorrect | Background Correction |
bgcorrect.gc | Background Correction |
bgcorrect.mas4 | Background Correction |
bgcorrect.mas5 | Background Correction |
bgcorrect.rma | Background Correction |
bgtreeNames | Class DataTreeSet |
bgtreeNames-method | Class DataTreeSet |
biopsyInfo | Class ProjectInfo |
biopsyInfo-method | Class ProjectInfo |
biopsyInfo<- | Class ProjectInfo |
biopsyInfo<--method | Class ProjectInfo |
borderplot | Plots of Border Elements |
borderplot-method | Class QualTreeSet |
borderplot-methods | Plots of Border Elements |
borders | Class QualTreeSet |
borders-method | Class QualTreeSet |
boxplot | Box Plots |
boxplot-method | Class ProcesSet |
boxplot-methods | Box Plots |
callFilter | Detection Call Filter |
callFilter-method | Class PreFilter |
callFilter-method | Class UniFilter |
callFilter-methods | Detection Call Filter |
callFilter<- | Detection Call Filter |
callFilter<--method | Class PreFilter |
callFilter<--method | Class UniFilter |
callplot | Barplot of Percent Present and Absent Calls. |
callplot-method | Class CallTreeSet |
callplot-methods | Barplot of Percent Present and Absent Calls. |
CallTreeSet | Class CallTreeSet |
callTreeset | Class FilterTreeSet |
CallTreeSet-class | Class CallTreeSet |
callTreeset-method | Class FilterTreeSet |
cellineInfo | Class ProjectInfo |
cellineInfo-method | Class ProjectInfo |
cellineInfo<- | Class ProjectInfo |
cellineInfo<--method | Class ProjectInfo |
chipMask | Class SchemeTreeSet |
chipMask-method | Class SchemeTreeSet |
chipMask<- | Class SchemeTreeSet |
chipMask<--method | Class SchemeTreeSet |
chipName | Class SchemeTreeSet |
chipName-method | Class ProcesSet |
chipName-method | Class SchemeTreeSet |
chipProbe | Class SchemeTreeSet |
chipProbe-method | Class SchemeTreeSet |
chipProbe<- | Class SchemeTreeSet |
chipProbe<--method | Class SchemeTreeSet |
chipType | Class SchemeTreeSet |
chipType-method | Class ProcesSet |
chipType-method | Class SchemeTreeSet |
chipType<- | Class SchemeTreeSet |
chipType<--method | Class SchemeTreeSet |
coiplot | Center-Of-Intensity QC Plots |
coiplot-method | Class QualTreeSet |
coiplot-methods | Center-Of-Intensity QC Plots |
corplot | Array-Array Expression Level Correlation Plot |
corplot-method | Class ExprTreeSet |
corplot-methods | Array-Array Expression Level Correlation Plot |
cvFilter | Coefficient of Variation Filter |
cvFilter-method | Class PreFilter |
cvFilter-methods | Coefficient of Variation Filter |
cvFilter<- | Coefficient of Variation Filter |
cvFilter<--method | Class PreFilter |
dabg.call | Detection Above Background Call |
datasetInfo | Class ProjectInfo |
datasetInfo-method | Class ProjectInfo |
datasetInfo<- | Class ProjectInfo |
datasetInfo<--method | Class ProjectInfo |
DataTreeSet | Class DataTreeSet |
DataTreeSet-class | Class DataTreeSet |
debug.xps | xps Options |
dfw | Distribution Free Weighted Expression Measure |
diffFilter | Difference Filter |
diffFilter-method | Class PreFilter |
diffFilter-methods | Difference Filter |
diffFilter<- | Difference Filter |
diffFilter<--method | Class PreFilter |
existsROOTFile | Test for Existing ROOT File |
exonLevel | Conversion of Parameter exonlevel to Integer |
export | Export data as text files |
export-method | Class ProcesSet |
export-method | Class SchemeTreeSet |
export-method | Class TreeSet |
export-methods | Export data as text files |
export.call | Export data as text files |
export.data | Export data as text files |
export.expr | Export data as text files |
export.filter | Export filter data as text files |
export.root | Export data from ROOT file |
export.scheme | Export data as text files |
express | Compute expression levels from raw data |
exprs | Get/Set Expression Values |
exprs-method | Class ExprTreeSet |
exprs-methods | Get/Set Expression Values |
exprs<- | Get/Set Expression Values |
exprs<--method | Class ExprTreeSet |
ExprTreeSet | Class ExprTreeSet |
exprTreeset | Class FilterTreeSet |
ExprTreeSet-class | Class ExprTreeSet |
exprTreeset-method | Class FilterTreeSet |
exprType | Class ExprTreeSet |
exprType-method | Class ExprTreeSet |
exprType<- | Class ExprTreeSet |
exprType<--method | Class ExprTreeSet |
extenPart | Get Extension of Tree Names |
farms | Factor Analysis for Robust Microarray Summarization Expression Measure |
fcFilter | Fold-Change Filter |
fcFilter-method | Class UniFilter |
fcFilter-methods | Fold-Change Filter |
fcFilter<- | Fold-Change Filter |
fcFilter<--method | Class UniFilter |
fileDir | Class TreeSet |
fileDir-method | Class TreeSet |
fileDir<- | Class TreeSet |
fileDir<--method | Class TreeSet |
Filter-class | Base Class Filter |
FilterTreeSet | Class FilterTreeSet |
filterTreeset | Class AnalysisTreeSet |
FilterTreeSet-class | Class FilterTreeSet |
filterTreeset-method | Class AnalysisTreeSet |
firma | Finding Isoforms using Robust Multichip Analysis |
firma.expr | Get Expression Levels from FIRMA |
firma.score | Get Splice Score from FIRMA |
fitQC | Functions for fitting probe-level models |
fitRLM | Functions for fitting RMA as probe-level model |
gapFilter | Gap Filter |
gapFilter-method | Class PreFilter |
gapFilter-methods | Gap Filter |
gapFilter<- | Gap Filter |
gapFilter<--method | Class PreFilter |
getChipName | Get Chip Name |
getChipType | Get Chip Type |
getDatatype | Get Data Type |
getNameType | Get Chip Name and Type |
getNumberTrees | Get Number of Trees |
getProbeInfo | Get Probe Information |
getTreeData | Export Tree Data |
getTreeData-method | Class AnalysisTreeSet |
getTreeData-method | Class FilterTreeSet |
getTreeData-method | Class ProcesSet |
getTreeData-methods | Export Tree Data |
getTreeNames | Get Tree Names |
highFilter | Upper Threshold Filter |
highFilter-method | Class PreFilter |
highFilter-methods | Upper Threshold Filter |
highFilter<- | Upper Threshold Filter |
highFilter<--method | Class PreFilter |
hist | Plot Density Estimate |
hist-method | Class DataTreeSet |
hist-method | Class ProcesSet |
hist-methods | Plot Density Estimate |
hybridizInfo | Class ProjectInfo |
hybridizInfo-method | Class ProjectInfo |
hybridizInfo<- | Class ProjectInfo |
hybridizInfo<--method | Class ProjectInfo |
image | Display an Image |
image-method | Class ProcesSet |
image-method | Class QualTreeSet |
image-methods | Display an Image |
import.data | Import CEL files into a DataTreeSet |
import.exon.scheme | Import CLF, PGF and annotation files into a SchemeTreeSet |
import.expr.scheme | Import CDF, probe and annotation files into a SchemeTreeSet |
import.genome.scheme | Import CLF, PGF and annotation files into a SchemeTreeSet |
indexUnits | Unit Locations |
indexUnits-method | Class DataTreeSet |
indexUnits-methods | Unit Locations |
ini.call | Informative/Non-Informative Call |
initialize | Initialize Classes |
initialize-method | Initialize Classes |
initialize-methods | Initialize Classes |
intensity | Get/Set Data Values |
intensity-method | Class DataTreeSet |
intensity-methods | Get/Set Data Values |
intensity2GCplot | Boxlot of Probe Intensities Stratified by GC Content. |
intensity2GCplot-method | Class DataTreeSet |
intensity2GCplot-methods | Boxlot of Probe Intensities Stratified by GC Content. |
intensity<- | Get/Set Data Values |
intensity<--method | Class DataTreeSet |
isROOTFile | Test for ROOT File |
lowFilter | Lower Threshold Filter |
lowFilter-method | Class PreFilter |
lowFilter-methods | Lower Threshold Filter |
lowFilter<- | Lower Threshold Filter |
lowFilter<--method | Class PreFilter |
madFilter | Median Absolute Deviation Filter |
madFilter-method | Class PreFilter |
madFilter-methods | Median Absolute Deviation Filter |
madFilter<- | Median Absolute Deviation Filter |
madFilter<--method | Class PreFilter |
madplot | Array-Array Expression Level Distance Plot |
madplot-method | Class ExprTreeSet |
madplot-methods | Array-Array Expression Level Distance Plot |
mas4 | MAS 4.0 Expression Measure |
mas5 | MAS 5.0 Expression Measure |
mas5.call | MAS 5.0 Absolute Detection Call |
mboxplot | Box Plots of Relative M Values |
mboxplot-method | Class ProcesSet |
mboxplot-methods | Box Plots of Relative M Values |
metaProbesets | Create MetaProbeset File for APT |
mm | Methods for accessing perfect matches and mismatches |
mm-method | Class DataTreeSet |
mm-methods | Methods for accessing perfect matches and mismatches |
mmindex | Unit Locations |
mmindex-method | Class DataTreeSet |
mmindex-methods | Unit Locations |
mvaplot | M vs A Plot |
mvaplot-method | Class ExprTreeSet |
mvaplot-methods | M vs A Plot |
namePart | Get Tree Names w/o Extension |
ncols | Class SchemeTreeSet |
ncols-method | Class DataTreeSet |
ncols-method | Class SchemeTreeSet |
normalize | Normalization on Affymetrix Probe Level Data or on Expression Levels |
normalize.constant | Normalization on Affymetrix Probe Level Data or on Expression Levels |
normalize.lowess | Normalization on Affymetrix Probe Level Data or on Expression Levels |
normalize.quantiles | Normalization on Affymetrix Probe Level Data or on Expression Levels |
normalize.supsmu | Normalization on Affymetrix Probe Level Data or on Expression Levels |
normType | Class ExprTreeSet |
normType-method | Class ExprTreeSet |
normType<- | Class ExprTreeSet |
normType<--method | Class ExprTreeSet |
nrows | Class SchemeTreeSet |
nrows-method | Class DataTreeSet |
nrows-method | Class SchemeTreeSet |
numberFilters | Base Class Filter |
numberFilters-method | Base Class Filter |
NUSE | Normalized Unscaled Standard Errors (NUSE) |
NUSE-method | Class QualTreeSet |
NUSE-methods | Normalized Unscaled Standard Errors (NUSE) |
nuseplot | Box Plots of Normalized Unscaled Standard Errors (NUSE) |
nuseplot-method | Class ExprTreeSet |
nuseplot-method | Class QualTreeSet |
nuseplot-methods | Box Plots of Normalized Unscaled Standard Errors (NUSE) |
pcaplot | PCA Plot |
pcaplot-method | Class ExprTreeSet |
pcaplot-methods | PCA Plot |
plotAffyRNAdeg | Functions to assess RNA Degradation. |
plotBorder | Plots of Border Elements for Device |
plotBoxplot | Box Plots for Device |
plotCall | Barplot of Percent Present and Absent Calls for Device |
plotCOI | Center-Of-Intensity QC Plots for Device |
plotCorr | Array-Array Expression Level Correlation Plot for Device |
plotDensity | Plot Density Estimate for Device |
plotImage | Plot Image(s) for Device |
plotIntensity2GC | Boxlot of Probe Intensities Stratified by GC Content for Device. |
plotMA | MvA Scatter Plot for Device |
plotMAD | Array-Array Expression Level Distance Plot for Device |
plotNUSE | Box Plots of Normalized Unscaled Standard Errors (NUSE) for Device |
plotPCA | PCA Plot for Device |
plotPM | Barplot of PM and MM Intensities for Device |
plotProbeset | Plot of Probe Intensities for a Probeset for Device. |
plotRLE | Box Plots of Relative Log Expression (RLE) for Device |
plotVolcano | Volcano Plot |
pm | Methods for accessing perfect matches and mismatches |
pm-method | Class DataTreeSet |
pm-methods | Methods for accessing perfect matches and mismatches |
pmindex | Unit Locations |
pmindex-method | Class DataTreeSet |
pmindex-methods | Unit Locations |
pmplot | Barplot of PM and MM Intensities. |
pmplot-method | Class DataTreeSet |
pmplot-methods | Barplot of PM and MM Intensities. |
PreFilter | Constructor for Class PreFilter |
prefilter | Function for Applying a PreFilter to an ExprTreeSet |
PreFilter-class | Class PreFilter |
presCall | Get/Set Present Call Values |
presCall-method | Class CallTreeSet |
presCall-methods | Get/Set Present Call Values |
presCall<- | Get/Set Present Call Values |
presCall<--method | Class CallTreeSet |
primcellInfo | Class ProjectInfo |
primcellInfo-method | Class ProjectInfo |
primcellInfo<- | Class ProjectInfo |
primcellInfo<--method | Class ProjectInfo |
probeContentGC | Get G/C Content for Probes |
probeContentGC-method | Class SchemeTreeSet |
probeContentGC-methods | Get G/C Content for Probes |
probeInfo | Class SchemeTreeSet |
probeInfo-method | Class SchemeTreeSet |
probeSequence | Get Probe Sequence |
probeSequence-method | Class SchemeTreeSet |
probeSequence-methods | Get Probe Sequence |
probesetID2unitID | Conversion between Probeset IDs and UnitIDs |
probesetID2unitID-method | Class DataTreeSet |
probesetID2unitID-method | Class SchemeTreeSet |
probesetID2unitID-methods | Conversion between Probeset IDs and UnitIDs |
probesetplot | Plot of Probe Intensities for a Probeset. |
probesetplot-method | Class DataTreeSet |
probesetplot-methods | Plot of Probe Intensities for a Probeset. |
ProcesSet | Class ProcesSet |
ProcesSet-class | Class ProcesSet |
ProjectInfo | Constructor for Class ProjectInfo |
projectInfo | Class ProjectInfo |
ProjectInfo-class | Class ProjectInfo |
projectInfo-method | Class DataTreeSet |
projectInfo-method | Class ProjectInfo |
projectInfo<- | Class ProjectInfo |
projectInfo<--method | Class DataTreeSet |
projectInfo<--method | Class ProjectInfo |
pvalData | Get/Set Present Call Values |
pvalData-method | Class CallTreeSet |
pvalData-methods | Get/Set Present Call Values |
pvalData<- | Get/Set Present Call Values |
pvalData<--method | Class CallTreeSet |
qualify | Probe Set Quality Control Functions |
qualify.rlm | Probe Set Quality Control Functions |
qualOption | Class QualTreeSet |
qualOption-method | Class QualTreeSet |
qualOption<- | Class QualTreeSet |
qualOption<--method | Class QualTreeSet |
QualTreeSet | Class QualTreeSet |
QualTreeSet-class | Class QualTreeSet |
qualType | Class QualTreeSet |
qualType-method | Class QualTreeSet |
qualType<- | Class QualTreeSet |
qualType<--method | Class QualTreeSet |
quantileFilter | Quantile Filter |
quantileFilter-method | Class PreFilter |
quantileFilter-methods | Quantile Filter |
quantileFilter<- | Quantile Filter |
quantileFilter<--method | Class PreFilter |
ratioFilter | Ratio Filter |
ratioFilter-method | Class PreFilter |
ratioFilter-methods | Ratio Filter |
ratioFilter<- | Ratio Filter |
ratioFilter<--method | Class PreFilter |
rawCELName | Method for getting names of the raw CEL-files |
rawCELName-method | Class DataTreeSet |
rawCELName-methods | Method for getting names of the raw CEL-files |
removeBgrd | Attach/Remove Background Intensities |
removeBgrd-method | Class DataTreeSet |
removeBgrd-methods | Attach/Remove Background Intensities |
removeCall | Attach/Remove Detecion Call Measures |
removeCall-method | Class CallTreeSet |
removeCall-methods | Attach/Remove Detecion Call Measures |
removeData | Attach/Remove Data |
removeData-method | Class ProcesSet |
removeData-methods | Attach/Remove Data |
removeDataXY | Attach/Remove (X,Y)-Coordinates |
removeDataXY-method | Class DataTreeSet |
removeDataXY-methods | Attach/Remove (X,Y)-Coordinates |
removeExpr | Attach/Remove Expression Measures |
removeExpr-method | Class ExprTreeSet |
removeExpr-methods | Attach/Remove Expression Measures |
removeInten | Attach/Remove Intensities |
removeInten-method | Class DataTreeSet |
removeInten-methods | Attach/Remove Intensities |
removeMask | Attach/Remove Scheme Mask |
removeMask-method | Class DataTreeSet |
removeMask-method | Class SchemeTreeSet |
removeMask-methods | Attach/Remove Scheme Mask |
removeProbe | Attach/Remove Probe Sequence and/or GC Content |
removeProbe-method | Class SchemeTreeSet |
removeProbeContentGC | Attach/Remove Probe Sequence and/or GC Content |
removeProbeContentGC-method | Class DataTreeSet |
removeProbeContentGC-method | Class SchemeTreeSet |
removeProbeContentGC-methods | Attach/Remove Probe Sequence and/or GC Content |
removeProbeSequence | Attach/Remove Probe Sequence and/or GC Content |
removeProbeSequence-method | Class SchemeTreeSet |
removeProbeSequence-methods | Attach/Remove Probe Sequence and/or GC Content |
removePVal | Attach/Remove Detecion Call Measures |
removePVal-method | Class CallTreeSet |
removePVal-methods | Attach/Remove Detecion Call Measures |
removeUnitNames | Attach/Remove Unit Names |
removeUnitNames-method | Class DataTreeSet |
removeUnitNames-method | Class SchemeTreeSet |
removeUnitNames-methods | Attach/Remove Unit Names |
residuals | Class QualTreeSet |
residuals-method | Class QualTreeSet |
RLE | Relative Log Expression (RLE) |
RLE-method | Class QualTreeSet |
RLE-methods | Relative Log Expression (RLE) |
rleplot | Box Plots of Relative Log Expression (RLE) |
rleplot-method | Class ExprTreeSet |
rleplot-method | Class QualTreeSet |
rleplot-methods | Box Plots of Relative Log Expression (RLE) |
rma | Robust Multi-Array Average Expression Measure |
rmaPLM | Functions for fitting RMA as probe-level model |
ROOT | ROOT An Object-Oriented Data Analysis Framework |
root.browser | Open the ROOT object browser |
root.browser-method | Class TreeSet |
root.call | Create class CallTreeSet accessing ROOT detection call file |
root.data | Create class DataTreeSet accessing ROOT data file |
root.density | ROOT Density Plot |
root.expr | Create class ExprTreeSet accessing ROOT expression file |
root.graph1D | ROOT 1D-Graph |
root.graph2D | ROOT 2D-Graph |
root.hist1D | ROOT 1D-Histogram |
root.hist2D | ROOT 2D-Histogram |
root.hist3D | ROOT 3D-Histogram |
root.image | ROOT Image |
root.merge.data | Create class DataTreeSet by merging ROOT data files |
root.mvaplot | ROOT M vs A Plot |
root.profile | ROOT Profile Plot |
root.scheme | Create class SchemeTreeSet accessing ROOT scheme file |
rootFile | Class TreeSet |
rootFile-method | Class TreeSet |
rootFile<- | Class TreeSet |
rootFile<--method | Class TreeSet |
sampleInfo | Class ProjectInfo |
sampleInfo-method | Class ProjectInfo |
sampleInfo<- | Class ProjectInfo |
sampleInfo<--method | Class ProjectInfo |
schemeFile | Class ProcesSet |
schemeFile-method | Class ProcesSet |
schemeFile<- | Class ProcesSet |
schemeFile<--method | Class ProcesSet |
schemeSet | Class ProcesSet |
schemeSet-method | Class ProcesSet |
schemeSet<- | Class ProcesSet |
schemeSet<--method | Class ProcesSet |
SchemeTreeSet | Class SchemeTreeSet |
SchemeTreeSet-class | Class SchemeTreeSet |
se.exprs | Class ExprTreeSet |
se.exprs-method | Class ExprTreeSet |
setName | Class TreeSet |
setName-method | Class TreeSet |
setName<- | Class TreeSet |
setName<--method | Class TreeSet |
setType | Class TreeSet |
setType-method | Class TreeSet |
setType<- | Class TreeSet |
setType<--method | Class TreeSet |
show-method | Class ProjectInfo |
sourceInfo | Class ProjectInfo |
sourceInfo-method | Class ProjectInfo |
sourceInfo<- | Class ProjectInfo |
sourceInfo<--method | Class ProjectInfo |
summarize | Probe Set Summarizing Functions |
summarize.mas4 | Probe Set Summarizing Functions |
summarize.mas5 | Probe Set Summarizing Functions |
summarize.rma | Probe Set Summarizing Functions |
summaryAffyRNAdeg | Functions to assess RNA Degradation. |
symbol2unitID | Conversion between Gene Symbols and UnitIDs |
symbol2unitID-method | Class DataTreeSet |
symbol2unitID-method | Class SchemeTreeSet |
symbol2unitID-methods | Conversion between Gene Symbols and UnitIDs |
tissueInfo | Class ProjectInfo |
tissueInfo-method | Class ProjectInfo |
tissueInfo<- | Class ProjectInfo |
tissueInfo<--method | Class ProjectInfo |
transcriptID2unitID | Conversion between Probeset IDs and UnitIDs |
transcriptID2unitID-method | Class DataTreeSet |
transcriptID2unitID-method | Class SchemeTreeSet |
transcriptID2unitID-methods | Conversion between Probeset IDs and UnitIDs |
treatmentInfo | Class ProjectInfo |
treatmentInfo-method | Class ProjectInfo |
treatmentInfo<- | Class ProjectInfo |
treatmentInfo<--method | Class ProjectInfo |
treeData | Class ProcesSet |
treeData-method | Class ProcesSet |
treeInfo | Get UserInfo from ROOT Trees |
treeInfo-method | Class TreeSet |
treeInfo-methods | Get UserInfo from ROOT Trees |
treeNames | Class TreeSet |
treeNames-method | Class TreeSet |
TreeSet | Class TreeSet |
TreeSet-class | Class TreeSet |
trma | transposed Robust Multi-Array Average Expression Measure |
type2Exten | Convert Method Type to Tree Extension |
UniFilter | Constructor for Class UniFilter |
unifilter | Function for Applying an UniFilter to an ExprTreeSet |
UniFilter-class | Class UniFilter |
uniTest | A Two-Group Unitest |
uniTest-method | Class UniFilter |
uniTest-methods | A Two-Group Unitest |
uniTest<- | A Two-Group Unitest |
uniTest<--method | Class UniFilter |
unitestFilter | Unitest Filter |
unitestFilter-method | Class UniFilter |
unitestFilter-methods | Unitest Filter |
unitestFilter<- | Unitest Filter |
unitestFilter<--method | Class UniFilter |
unitID2probesetID | Conversion between Probeset IDs and UnitIDs |
unitID2probesetID-method | Class DataTreeSet |
unitID2probesetID-method | Class SchemeTreeSet |
unitID2probesetID-methods | Conversion between Probeset IDs and UnitIDs |
unitID2symbol | Conversion between Gene Symbols and UnitIDs |
unitID2symbol-method | Class DataTreeSet |
unitID2symbol-method | Class SchemeTreeSet |
unitID2symbol-methods | Conversion between Gene Symbols and UnitIDs |
unitID2transcriptID | Conversion between Probeset IDs and UnitIDs |
unitID2transcriptID-method | Class DataTreeSet |
unitID2transcriptID-method | Class SchemeTreeSet |
unitID2transcriptID-methods | Conversion between Probeset IDs and UnitIDs |
unitNames | Class SchemeTreeSet |
unitNames-method | Class SchemeTreeSet |
unitNames<- | Class SchemeTreeSet |
unitNames<--method | Class SchemeTreeSet |
validBgrd | Class DataTreeSet |
validBgrd-method | Class DataTreeSet |
validCall | Get Valid Detection Call Values |
validCall-method | Class CallTreeSet |
validData | Extract Subset of Data |
validData-method | Class AnalysisTreeSet |
validData-method | Class DataTreeSet |
validData-method | Class FilterTreeSet |
validData-method | Class ProcesSet |
validExpr | Get Valid Expression Levels |
validExpr-method | Class ExprTreeSet |
validFilter | Class AnalysisTreeSet |
validFilter-method | Class AnalysisTreeSet |
validPVal | Get Valid Detection Call Values |
validPVal-method | Class CallTreeSet |
validSE | Get Valid Standard Errors |
validSE-method | Class ExprTreeSet |
validTreetype | Validate Tree Type |
varFilter | Variance Filter |
varFilter-method | Class PreFilter |
varFilter-methods | Variance Filter |
varFilter<- | Variance Filter |
varFilter<--method | Class PreFilter |
volcanoplot | Volcano Plot |
volcanoplot-method | Class AnalysisTreeSet |
volcanoplot-methods | Volcano Plot |
weights | Class QualTreeSet |
weights-method | Class QualTreeSet |
xps | xps Package Overview |
xpsBgCorrect | Background Correction |
xpsBgCorrect-method | Class DataTreeSet |
xpsBgCorrect-methods | Background Correction |
xpsDABGCall | Detection Above Background Call |
xpsDABGCall-method | Class DataTreeSet |
xpsDABGCall-methods | Detection Above Background Call |
xpsFIRMA | Finding Isoforms using Robust Multichip Analysis |
xpsFIRMA-method | Class DataTreeSet |
xpsFIRMA-methods | Finding Isoforms using Robust Multichip Analysis |
xpsINICall | Informative/Non-Informative Call |
xpsINICall-method | Class DataTreeSet |
xpsINICall-methods | Informative/Non-Informative Call |
xpsMAS4 | MAS 4.0 Expression Measure |
xpsMAS4-method | Class DataTreeSet |
xpsMAS4-methods | MAS 4.0 Expression Measure |
xpsMAS5 | MAS 5.0 Expression Measure |
xpsMAS5-method | Class DataTreeSet |
xpsMAS5-methods | MAS 5.0 Expression Measure |
xpsMAS5Call | MAS 5.0 Absolute Detection Call |
xpsMAS5Call-method | Class DataTreeSet |
xpsMAS5Call-methods | MAS 5.0 Absolute Detection Call |
xpsNormalize | Normalization on Affymetrix Probe Level Data or on Expression Levels |
xpsNormalize-method | Class DataTreeSet |
xpsNormalize-method | Class ExprTreeSet |
xpsNormalize-methods | Normalization on Affymetrix Probe Level Data or on Expression Levels |
xpsOptions | xps Options |
xpsPreFilter | Function for Applying a PreFilter to an ExprTreeSet |
xpsPreFilter-method | Class ExprTreeSet |
xpsPreFilter-methods | Function for Applying a PreFilter to an ExprTreeSet |
xpsPreprocess | Compute expression levels from raw data |
xpsPreprocess-method | Class DataTreeSet |
xpsPreprocess-methods | Compute expression levels from raw data |
xpsQAReport | Create Quality Assessment Report. |
xpsQualify | Probe Set Quality Control Functions |
xpsQualify-method | Class DataTreeSet |
xpsQualify-methods | Probe Set Quality Control Functions |
xpsQualityControl | Functions for fitting probe-level models |
xpsQualityControl-method | Class DataTreeSet |
xpsQualityControl-methods | Functions for fitting probe-level models |
xpsRMA | Robust Multi-Array Average Expression Measure |
xpsRMA-method | Class DataTreeSet |
xpsRMA-methods | Robust Multi-Array Average Expression Measure |
xpsRNAdeg | Functions to assess RNA Degradation. |
xpsRNAdeg-method | Class QualTreeSet |
xpsRNAdeg-methods | Functions to assess RNA Degradation. |
xpsSummarize | Probe Set Summarizing Functions |
xpsSummarize-method | Class DataTreeSet |
xpsSummarize-methods | Probe Set Summarizing Functions |
xpsUniFilter | Function for Applying an UniFilter to an ExprTreeSet |
xpsUniFilter-method | Class ExprTreeSet |
xpsUniFilter-methods | Function for Applying an UniFilter to an ExprTreeSet |