/usr/lib/R/site-library/affy/INDEX is in r-bioc-affy 1.52.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 | .setAffyOptions ~~function to set options ~~
AffyBatch-class Class AffyBatch
AffyRNAdeg Function to assess RNA degradation in
Affymetrix GeneChip data.
MAplot Relative M vs. A plots
ProbeSet-class Class ProbeSet
ProgressBarText-class Class "ProgressBarText"
SpikeIn SpikeIn Experiment Data: ProbeSet Example
affy-options Options for the affy package
affy.scalevalue.exprSet
Scale normalization for expreSets
barplot.ProbeSet show a ProbeSet as barplots
bg.adjust Background adjustment (internal function)
bg.correct Background Correction
cdfFromBioC Functions to obtain CDF files
cdfenv.example Example cdfenv
cleancdfname Clean Affymetrix's CDF name
debug.affy123 Debugging Flag
express.summary.stat 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
generateExprSet-methods
generate a set of expression values
generateExprVal.method.avgdiff
Generate an expression value from the probes
informations
generateExprVal.method.playerout
Generate an expression value from the probes
informations
hlog Hybrid Log
justRMA Read CEL files into an ExpressionSet
list.celfiles List the Cel Files in a Directory/Folder
loess.normalize Deprecated functions in package 'affy'
mas5 MAS 5.0 expression measure
mas5calls MAS 5.0 Absolute Detection
merge.AffyBatch merge two AffyBatch objects
mva.pairs M vs. A Matrix
normalize.AffyBatch Normalize Affymetrix Probe Level Data - methods
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
Invariant Set normalization
normalize.loess Scale microarray data
normalize.qspline Normalize arrays
pairs.AffyBatch plot intensities using 'pairs'
plot.ProbeSet plot a probe set
plotDensity Plot Densities
plotLocation Plot a location on a cel image
pmcorrect PM Correction
ppsetApply Apply a function over the ProbeSets in an
AffyBatch
probeMatch-methods Methods for accessing perfect matches and
mismatches
probeNames-methods Methods for accessing the Probe Names
read.affybatch Read CEL files into an AffyBatch
read.probematrix Read CEL file data into PM or MM matrices
rma Robust Multi-Array Average expression measure
summary Probe Set Summarizing Functions
tukey.biweight One-step Tukey's biweight
whatcdf Find which CDF corresponds
xy2indices Functions to convert indices to x/y (and
reverse)
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