Class ProbeSet
generateExprVal.method.avgdiff
Generate an expression value from the probes informations
Example cdfenv
normalize.quantiles.robust
Robust Quantile Normalization
List the Cel Files in a Directory/Folder
M vs. A Matrix
plotILM
Assessment Plots
Methods for accessing the Probe Names
SD Assessment functions
Remove crosshybridizers
Function to assess RNA degradation in Affymetrix GeneChip data.
Deprecated functions in package ‘affy’
Assessment functions
Probe Set Summarizing Functions
Internal affyPLM functions
Example of the result of assessments
affycomp.figures.auxiliary
Auxiliary functions to create Figures
generateExprVal.method.pdnn
Compute PM correction and summary expression value
affyILM
A Function to Automagically Place a Legend in a PCA Plot
QC report title page with array names
Take log base 2 of Expression
Scale probe intensities
Invariant Set normalization
Normalize arrays
New Assessment functions for Spike In Data
Robust Multi-Array Average expression measure
Parallelized PMA preprocessing
Make repetitive analyses of microarray and RNA-Seq data simpler with affycoretools.
Compute a summary expression value from the probes intensities
Create Indices for Venn Diagrams
A function to create a simple heatmap and key.
Functions to obtain CDF files
normalizeAffyBatchLoessIterPara
Parallelized partial loess normalization with permutation
Parallel fir of the vsn model
Read CEL files into an ExpressionSet
normalizeAffyBatchConstantPara
Parallelized scaling normalization
Relative M vs. A plots
SD Assessment Functions
Plot the PDNN computed probe intensities
Class to contain the results of an ilm calculation
Coloring pseudo chip images
Parallelized relative M vs. A plots for Microarray Data
Read RMAExpress computed expression values
4-way Venn Diagrams
Position Dependant Nearest Neighbors model for affy
Parallel generate a set of expression values
affycomp.compfigs.auxiliary
Auxiliary functions to create comparitive Figures
A Function to Make a Classlabel Vector for Plotting
SpikeIn Experiment Data: ProbeSet Example
Fit Li and Wong Model to a Probe Set
From raw probe intensities to expression values
Scale microarray data
Plot a location on a cel image
Merge a list of split objects
Read CEL files into an AffyBatch
Distribute files to slaves
Parallelized Read-AffyBatch function
plotIntens
Remove distributed files from slaves
Normalization applied to ExpressionSets
Pre-processing for Affymetrix Data
Three Step expression measures returned as a PLMset
QC Report for AffyBatch objects
Remove control probesets from ST arrays
Functions to Plot Density and RNA Degradation Plots
affylmGUI Change Log
A function to create an HTML page for each gene set, as well as the HTML
pages for each significant gene set.
A function to fit PDNN parameters
A function to create a heatmap-like object or matrix of correlations between
miRNA and mRNA data.
A function to run the romer function on a set of contrasts.
Extract Dates from CEL files
Chip-type specific data
A function to find the experiment specific PDNN parameters
Read header information from cel file
A function to transform a ProbeSet
Clean Affymetrix's CDF name
Plot Densities
PM Correction
Apply a function over the ProbeSets in an AffyBatch
Quantile Normalization
Functions to convert indices to x/y (and reverse)
Class AffyBatch
LESN - Low End Signal is Noise Background corrections
Options for the affy package
hgu133a.spikein.phenodata
phenotypic information for HGU133A spike in study
CDF file format function
Assessment functions for Spike In Data
Background adjustment (internal function)
Hybrid Log
Class "ProgressBarText"
Normalize intensities using the contrasts method
One-step Tukey's biweight
Three Step expression measures
Scale normalization for expreSets
Normalize Affymetrix Probe Level Data - methods
Functions to split objects into parts
Convert a PLMset to an ExpressionSet
Center of intensity QC plots
Parallelized Box Plots for Microarray Data
Create HTML tables for Gene Ontology (GO) analyses
Method to annotate ExpressionSets automatically
Assessment functions for Dilution Data
normalizeAffyBatchLoessPara
Parallelized loess normalization
normalize.quantiles.probeset
Quantile Normalization applied to probesets
A function to map miRNA to mRNA.
Correct Ordering of Contrasts
Fit a RMA to Affymetrix Genechip Data as a PLMset
Compute Counts for Venn Diagram
Select and Output Genelists Based on Venn Diagrams
Graphical User Interface for the limma microarray package
show a ProbeSet as barplots
generateExprVal.method.playerout
Generate an expression value from the probes informations
Select Subset
plot a probe set
set a rectangular or circular region in an affybatch to a
specified set of values
Background correct and Normalize
Scaling normalization
Read CEL file data into PM or MM matrices
generate a set of expression values
MAS 5.0 expression measure
Parallel Quality Assessment Summary
Methods to access the results of ilm.
Methods for accessing perfect matches and mismatches
~~function to set options ~~
Parallelized preprocessing
Expression Assessment Table
Intensity distribution plots for a AffyBatch object
Parallelized Background Correction
A widget for users to pick correction methods
Class to contain input data and parameters for parallel vsn functions
Starting and Stopping SNOW Clusters
normalizeAffyBatchInvariantsetPara
Parallelized Invariante Set normalization
High-level function for making Venn diagrams with clickable links to HTML
pages with the underlying genes.
Generate a QA Report for Affymetrix arrays
Parameters for the Dilution dataset
Make Gene table from GO analysis results
Filter a topTable object
normalizeAffyBatchQuantilesPara
Parallelized quantile normalization
Array-array intensity correlation plot
phenotypic information for spike in study
Create Names for Venn Diagram Intersections
Cross hybridizers
High-level function for making Venn diagrams and outputting the results from
the diagrams in HTML and CSV files.
Function to output annotated fit data from limma
read.celfile.probeintensity.matrices
Read PM or MM from CEL file into matrices
Background Correction
Debugging Flag
plot intensities using 'pairs'
merge two AffyBatch objects
Find which CDF corresponds
Fit a Probe Level Model to Affymetrix Genechip Data.
Class PLMset
MAS 5.0 Absolute Detection
Phenotypic Information for Dilution Study
Distribution of intensities of the border elements
A function to create an annotated HTML table for all genes in a significant
gene set as well as a heatmap of these data.
Add links to data when using ReportingTools
Read Expression Date Sets
Add dotplot images
Fix data.frame header for use with ReportingTools
Defunct functions in package affycoretools A Function to Make a PCA Plot from an ExpressionSet
Read a CEL file into an R list
A function to create HTML output from the results of running romer on a set
of contrasts.
Read CDF file into an R list