MAROBUSTMEANS procedure

Does a robust means analysis for Affymetrix slides (D.B. Baird).

Options

TRANSFORMATION = string

How to transform the data (log2, none); default none

MAXCYCLE = scalar

Maximum number of iterations; default 50

TOLERANCE = scalar

Tolerance for convergence; default 0.0001

Parameters

DATA = variates or pointers

Expression data to be summarized

SLIDES = factors

Defines the slides

PROBES = factors

Defines the probes

IDPROBES = factors

Saves the probe IDs

MEDIANS = variates

Saves the robust means

SEM = variates

Saves approximate standard errors of the robust means

Description

MAROBUSTMEANS calculates the medians of probe expression values across a series of Affymetrix slides. The median expression level for each slide is estimated and removed in a iterative fashion using an algorithm called the median polish algorithm. An approximate standard error of the mean can be calculated which is defined as 1.483 times the median absolute deviation from the probe medians.

The expression intensity values are supplied by the DATA parameter. If these are in a single variate, the SLIDE parameter should supply a factor to index the slides, and the PROBES parameter should index the probes or genes. Alternatively you can supply a pointer containing a variate for each The SLIDES factor is then not required; if it is given it should just have one entry for each slide in the order of the variates in the pointer. The PROBES factor is that for a single slide, and all slides must have a common layout.

Options: TRANSFORMATION, MAXCYCLE, TOLERANCE.

Parameters: DATA, SLIDES, PROBES, IDPROBES, MEDIANS, SEM.