Microarray data
There is a suite of procedures for the design, analysis and visualization of two-colour and
Affymetrix microarray data. These are used by the Microarray menus in GenStat for Windows.
generates balanced incomplete block designs
generates loop designs e.g. for time-course microarray
experiments
generates reference-level designs e.g. for microarray
experiments
assesses the efficiency of a two-colour microarray design
corrects and transforms two-colour microarray differential
expressions
normalizes two-colour microarray data
estimates treatment effects from a two-colour microarray
design
estimates expression values for Affymetrix slides.
performs background correction of Affymetrix slides
does a robust means analysis for Affymetrix slides
calculates Affymetrix expression values
applies the average difference algorithm to Affymetrix
data
plots the empirical CDF or PDF (kernel smoothed) by
groups
plots histograms of microarray data
produces two-dimensional plots of microarray data
produces shade plots to display spatial variation of microarray
data
produces volcano plots of microarray data
clusters probes or genes with microarray data
clusters microarray slides
performs a two-way clustering of microarray data by probes
(or genes) and slides
estimates false discovery rates using mixture distributions
modifies t-values by an empirical Bayes method.
performs a median polish of two-way data
performs quantile normalization
calculates the basis functions for thin-plate splines
estimates means using the Tukey biweight algorithm