Does a robust means analysis for Affymetrix slides (D.B. Baird).
Options
TRANSFORMATION = string token |
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 or texts |
Defines the slides |
PROBES = factors |
Defines the probes |
IDPROBES = factors |
Saves the probe IDs |
MEDIANS = variates or pointers |
Saves the robust means |
SEM = variates or pointers |
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 slide. The SLIDES parameter can be omitted, or it can supply a text to label the slides in the pointer. The PROBES factor refers to a single slide, and all the slides must have a common layout.
Options: TRANSFORMATION, MAXCYCLE, TOLERANCE.
Parameters: DATA, SLIDES, PROBES, IDPROBES, MEDIANS, SEM.
See also
Procedures: AFFYMETRIX, FDRBONFERRONI, FDRMIXTURE, MAANOVA, MABGCORRECT, MAEBAYES, MAREGRESSION, MARMA, MAVDIFFERENCE, MAVOLCANO, QNORMALIZE.
Commands for: Microarray data.
Example
CAPTION 'MAROBUSTMEANS example'; STYLE=meta
ENQUIRE CHANNEL=-1; EXIST=check; NAME=\
'%GENDIR%/Data/Microarrays/Hyb-Expressions.gsh'
IF check
SPLOAD '%GENDIR%/Data/Microarrays/Hyb-Expressions.gsh'
" Calculate robust means over Slides and Atoms for each probe."
MAROBUSTMEANS [TRANSFORM=none] Expression; SLIDES=Slides; PROBES=Probes;\
IDPROBES = ProbeID; MEDIANS = Exp_Medians; SEM = Exp_SE
FSPREADSHEET ProbeID,Exp_Medians,Exp_SE
ELSE
CAPTION 'Microarray example datasets have not been installed.'
ENDIF