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.

`AGBIB`	generates balanced incomplete block designs
`AGLOOP`	generates loop designs e.g. for time-course microarray experiments
`AGREFERENCE`	generates reference-level designs e.g. for microarray experiments
`BAFFYMETRIX`	Estimates expression values from an Affymetrix CED and CDF file
`MADESIGN`	assesses the efficiency of a two-colour microarray design
`MACALCULATE`	corrects and transforms two-colour microarray differential expressions
`MNORMALIZE`	normalizes two-colour microarray data
`MAESTIMATE`	estimates treatment effects from a two-colour microarray design
`AFFYMETRIX`	estimates expression values for Affymetrix slides.
`MABGCORRECT`	performs background correction of Affymetrix slides
`MAROBUSTMEANS`	does a robust means analysis for Affymetrix slides
`MARMA`	calculates Affymetrix expression values
`MAVDIFFERENCE`	applies the average difference algorithm to Affymetrix data
`DMADENSITY`	plots the empirical CDF or PDF (kernel smoothed) by groups
`MAHISTOGRAM`	plots histograms of microarray data
`MAPLOT`	produces two-dimensional plots of microarray data
`MAANOVA`	does analysis of variance of single-channel microarray data
`MAREGRESSION`	does regressions for single-channel microarray data
`MASHADE`	produces shade plots to display spatial variation of microarray data
`MAVOLCANO`	produces volcano plots of microarray data
`MAPCLUSTER`	clusters probes or genes with microarray data
`MASCLUSTER`	clusters microarray slides
`MA2CLUSTER`	performs a two-way clustering of microarray data by probes (or genes) and slides
`FDRBONFERRONI`	estimates false discovery rates by a Bonferroni-type procedure
`FDRMIXTURE`	estimates false discovery rates using mixture distributions
`MAEBAYES`	modifies t-values by an empirical Bayes method.
`MPOLISH`	performs a median polish of two-way data
`QNORMALIZE`	performs quantile normalization
`THINPLATE`	calculates the basis functions for thin-plate splines
`TUKEYBIWEIGHT`	estimates means using the Tukey biweight algorithm

Updated on May 20, 2019

Was this article helpful?

Yes No