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Expression Analysis

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

Functions

mattest Perform two-sample t-test to evaluate differential expression of genes from two experimental conditions or phenotypes
mafdr Estimate false discovery rate (FDR) for multiple hypothesis testing
mavolcanoplot Create significance versus gene expression ratio (fold change) scatter plot of microarray data
mairplot Create intensity versus ratio scatter plot of microarray data
maboxplot Create box plot for microarray data
maloglog Create loglog plot of microarray data
mapcaplot Create Principal Component Analysis (PCA) plot of microarray data
clustergram Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
redbluecmap Create red and blue colormap
redgreencmap Create red and green colormap
probesetplot Plot Affymetrix probe set intensity values
rankfeatures Rank key features by class separability criteria
randfeatures Generate randomized subset of features
knnclassify Classify data using nearest neighbor method
knnimpute Impute missing data using nearest-neighbor method
classperf Evaluate performance of classifier
crossvalind Generate cross-validation indices

Classes

DataMatrix Create DataMatrix object
DataMatrix object Data structure encapsulating data and metadata from microarray experiment so that it can be indexed by gene or probe identifiers and by sample identifiers
bioma.ExpressionSet Contain data from microarray gene expression experiment
bioma.data.ExptData Contain data values from microarray experiment
bioma.data.MetaData Contain metadata from microarray experiment
bioma.data.MIAME Contain experiment information from microarray gene expression experiment
HeatMap Display heat map of matrix data and create HeatMap object
HeatMap object Object containing matrix and heat map display properties
clustergram Compute hierarchical clustering, display dendrogram and heat map, and create clustergram object
clustergram object Object containing hierarchical clustering analysis data
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