A B C D E F G H I J L M N O P Q R S T U W X misc
$.AffyBatch | Class AffyBatch |
.setAffyOptions | ~~function to set options ~~ |
affy-options | Options for the affy package |
affy.scalevalue.exprSet | Scale normalization for expreSets |
AffyBatch | Class AffyBatch |
AffyBatch-class | Class AffyBatch |
affybatch.example | AffyBatch instance affybatch.example |
AffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data. |
avdiff | Probe Set Summarizing Functions |
barplot,ProbeSet-method | Class ProbeSet |
barplot.ProbeSet | show a ProbeSet as barplots |
bg.adjust | Background ajustment (internal function) |
bg.correct | Background Correction |
bg.correct,AffyBatch,character-method | Class AffyBatch |
bg.correct-methods | Background Correction |
bg.correct.mas | Background Correction |
bg.correct.methods | Background Correction |
bg.correct.none | Background Correction |
bg.correct.rma | Background Correction |
bg.correct.rma2 | Background Correction |
bg.parameters | Background ajustment (internal function) |
bgcorrect.methods | Background Correction |
boxplot,AffyBatch-method | Class AffyBatch |
cdfenv.example | Example cdfenv |
cdfFromBioC | Functions to obtain CDF files |
cdfFromData | Functions to obtain CDF files |
cdfFromEnvironment | Functions to obtain CDF files |
cdfFromLibPath | Functions to obtain CDF files |
cdfName | Class AffyBatch |
cdfName,AffyBatch-method | Class AffyBatch |
cleancdfname | Clean Affymetrix's CDF name |
close,ProgressBarText-method | Class "ProgressBarText" |
colnames,ProbeSet-method | Class ProbeSet |
computeExprSet | generate a set of expression values |
computeExprSet,AffyBatch,character,character-method | Class AffyBatch |
concentrations | SpikeIn Experiment Data: ProbeSet Example |
debug.affy123 | Debugging Flag |
express.summary.stat | Compute a summary expression value from the probes intensities |
express.summary.stat,ProbeSet,character,character-method | Class ProbeSet |
express.summary.stat-methods | Compute a summary expression value from the probes intensities |
express.summary.stat.methods | Compute a summary expression value from the probes intensities |
expresso | From raw probe intensities to expression values |
expressoWidget | A widget for users to pick correction methods |
fit.li.wong | Fit Li and Wong Model to a Probe Set |
geneNames | Class AffyBatch |
geneNames,AffyBatch-method | Class AffyBatch |
geneNames<-,AffyBatch-method | Class AffyBatch |
generateExprSet-methods | generate a set of expression values |
generateExprSet.methods | generate a set of expression values |
generateExprVal | Compute a summary expression value from the probes intensities |
generateExprVal-methods | Compute a summary expression value from the probes intensities |
generateExprVal.method.avgdiff | Generate an expression value from the probes informations |
generateExprVal.method.liwong | Generate an expression value from the probes informations |
generateExprVal.method.mas | Generate an expression value from the probes informations |
generateExprVal.method.medianpolish | Generate an expression value from the probes informations |
generateExprVal.method.playerout | Generate an expression value from the probes informations |
generateExprVal.methods | Compute a summary expression value from the probes intensities |
getCdfInfo | Class AffyBatch |
getCdfInfo,AffyBatch-method | Class AffyBatch |
hist,AffyBatch-method | Class AffyBatch |
hlog | Hybrid Log |
image | Class AffyBatch |
image,AffyBatch-method | Class AffyBatch |
indexProbes | Class AffyBatch |
indexProbes,AffyBatch,character-method | Class AffyBatch |
indexProbes,AffyBatch-method | Class AffyBatch |
indices2xy | Functions to convert indices to x/y (and reverse) |
initialize,ProgressBarText-method | Class "ProgressBarText" |
intensity | Class AffyBatch |
intensity,AffyBatch-method | Class AffyBatch |
intensity<-,AffyBatch-method | Class AffyBatch |
just.rma | Read CEL files into an AffyBatch |
justRMA | Read CEL files into an AffyBatch |
length,AffyBatch-method | Class AffyBatch |
li.wong | Fit Li and Wong Model to a Probe Set |
list.celfiles | List the Cel Files in a Directory/Folder |
loess.normalize | Normalize arrays |
ma.plot | Relative M vs. A plots |
mapCdfName | Clean Affymetrix's CDF name |
MAplot | Relative M vs. A plots |
MAplot,AffyBatch-method | Relative M vs. A plots |
mas5 | MAS 5.0 expression measure |
mas5.detection | MAS 5.0 Absolute Detection |
mas5calls | MAS 5.0 Absolute Detection |
mas5calls,AffyBatch-method | MAS 5.0 Absolute Detection |
mas5calls,ProbeSet-method | MAS 5.0 Absolute Detection |
mas5calls.AffyBatch | MAS 5.0 Absolute Detection |
mas5calls.ProbeSet | MAS 5.0 Absolute Detection |
Mbox | Relative M vs. A plots |
Mbox,AffyBatch-method | Relative M vs. A plots |
medianpolish | Probe Set Summarizing Functions |
merge.AffyBatch | merge two AffyBatch objects |
mm | Methods for accessing perfect matches and mismatches |
mm,AffyBatch-method | Class AffyBatch |
mm,ProbeSet-method | Class ProbeSet |
mm<-,AffyBatch,ANY-method | Class AffyBatch |
mm<-,ProbeSet,matrix-method | Class ProbeSet |
mmindex | Class AffyBatch |
mmindex,AffyBatch-method | Class AffyBatch |
mva.pairs | M vs. A Matrix |
ncol,AffyBatch-method | Class AffyBatch |
normalize | Normalize - generic |
normalize,AffyBatch-method | Normalize Affymetrix Probe Level Data - methods |
normalize.AffyBatch | Normalize Affymetrix Probe Level Data - methods |
normalize.AffyBatch.constant | Scale probe intensities |
normalize.AffyBatch.contrasts | Normalize intensities using the contrasts method |
normalize.AffyBatch.invariantset | Invariante Set normalization |
normalize.AffyBatch.loess | Scale microarray data |
normalize.AffyBatch.methods | Normalize Affymetrix Probe Level Data - methods |
normalize.AffyBatch.qspline | Normalize arrays |
normalize.AffyBatch.quantiles | Quantile Normalization |
normalize.AffyBatch.quantiles.robust | Robust Quantile Normalization |
normalize.constant | Scale probe intensities |
normalize.contrasts | Normalize intensities using the contrasts method |
normalize.invariantset | Invariante Set normalization |
normalize.loess | Scale microarray data |
normalize.methods | Normalize Affymetrix Probe Level Data - methods |
normalize.methods,AffyBatch-method | Normalize Affymetrix Probe Level Data - methods |
normalize.qspline | Normalize arrays |
normalize.quantiles | Quantile Normalization |
normalize.quantiles.robust | Robust Quantile Normalization |
nrow,AffyBatch-method | Class AffyBatch |
open,ProgressBarText-method | Class "ProgressBarText" |
pairs.AffyBatch | plot intensities using 'pairs' |
playerout.costfunction | Generate an expression value from the probes informations |
plot.ProbeSet | plot a probe set |
plotAffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data. |
plotDensity | Plot Densities |
plotLocation | Plot a location on a cel image |
pm | Methods for accessing perfect matches and mismatches |
pm,AffyBatch-method | Class AffyBatch |
pm,ProbeSet-method | Class ProbeSet |
pm<-,AffyBatch,ANY-method | Class AffyBatch |
pm<-,ProbeSet,matrix-method | Class ProbeSet |
pmcorrect | PM Correction |
pmindex | Class AffyBatch |
pmindex,AffyBatch-method | Class AffyBatch |
ppset.ttest | Apply a function over the ProbeSets in an AffyBatch |
ppsetApply | Apply a function over the ProbeSets in an AffyBatch |
probeMatch | Methods for accessing perfect matches and mismatches |
probeMatch-methods | Methods for accessing perfect matches and mismatches |
probeNames | Methods for accessing the Probe Names |
probeNames,AffyBatch-method | Class AffyBatch |
probeNames-methods | Methods for accessing the Probe Names |
probes | Class AffyBatch |
probes,AffyBatch-method | Class AffyBatch |
probeset | Class AffyBatch |
probeset,AffyBatch-method | Class AffyBatch |
ProbeSet-class | Class ProbeSet |
ProgressBarText-class | Class "ProgressBarText" |
qspline-normalize | Normalize arrays |
read.affybatch | Read CEL files into an AffyBatch |
read.probematrix | Read CEL file data into PM or MM matrices |
ReadAffy | Read CEL files into an AffyBatch |
rma | Robust Multi-Array Average expression measure |
sampleNames,ProbeSet-method | Class ProbeSet |
show,AffyBatch-method | Class AffyBatch |
show,ProbeSet-method | Class ProbeSet |
SpikeIn | SpikeIn Experiment Data: ProbeSet Example |
split.AffyBatch | split an AffyBatch |
summary | Probe Set Summarizing Functions |
summaryAffyRNAdeg | Function to assess RNA degradation in Affymetrix GeneChip data. |
tukey.biweight | One-step Tukey's biweight |
tukeybiweight | Probe Set Summarizing Functions |
update,ProgressBarText-method | Class "ProgressBarText" |
whatcdf | Find which CDF corresponds |
xy2indices | Functions to convert indices to x/y (and reverse) |
[,AffyBatch-method | Class AffyBatch |
[<-,AffyBatch-method | Class AffyBatch |
[[,AffyBatch-method | Class AffyBatch |