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Expression Analysis

Identify, visualize, and classify differentially expressed genes and expression profiles

Functions

mattestPerform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mafdrEstimate false discovery rate (FDR) for multiple hypothesis testing
mavolcanoplotCreate significance versus gene expression ratio (fold change) scatter plot of microarray data
mairplotCreate intensity versus ratio scatter plot of microarray data
maboxplotCreate box plot for microarray data
maloglogCreate loglog plot of microarray data
mapcaplotCreate Principal Component Analysis (PCA) plot of microarray data
nbintestUnpaired hypothesis test for count data with small sample sizes
clustergramCompute hierarchical clustering, display dendrogram and heat map, and create clustergram object
redbluecmapCreate red and blue colormap
redgreencmapCreate red and green colormap
probesetplotPlot Affymetrix probe set intensity values
metafeaturesAttractor metagene algorithm for feature engineering using mutual information-based learning
rankfeaturesRank key features by class separability criteria
randfeaturesGenerate randomized subset of features
knnimputeImpute missing data using nearest-neighbor method
classperfEvaluate performance of classifier
crossvalindGenerate cross-validation indices

Classes

DataMatrixCreate DataMatrix object
DataMatrix objectData structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
bioma.ExpressionSetContain data from microarray gene expression experiment
bioma.data.ExptDataContain data values from microarray experiment
bioma.data.MetaDataContain metadata from microarray experiment
bioma.data.MIAMEContain experiment information from microarray gene expression experiment
NegativeBinomialTestUnpaired hypothesis test result
HeatMapDisplay heat map of matrix data and create HeatMap object
HeatMap objectObject containing matrix and heat map display properties
clustergram objectObject containing hierarchical clustering analysis data

Topics

Analyzing Gene Expression Profiles

Analyze microarray data for patterns and plot the results.

Managing Gene Expression Data in Objects

Overview of objects for Microarray Gene Expression Data

Representing Expression Data Values in DataMatrix Objects

Construct DataMatrix objects, get and set properties, and access data.

Representing Expression Data Values in ExptData Objects

Construct ExptData objects, use properties and methods, and access data.

Representing Sample and Feature Metadata in MetaData Objects

Construct MetaData objects, use properties and methods, and access data.

Representing Experiment Information in a MIAME Object

Construct MIAME objects, use properties and methods, and access data.

Representing All Data in an ExpressionSet Object

Construct ExpressionSet objects, use properties and methods, and access data.

Exploring Microarray Gene Expression Data

This example shows how to identify differentially expressed genes from microarray data and uses Gene Ontology to determine significant biological functions that are associated to the down- and up-regulated genes.

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