Does a robust means analysis for Affymetrix slides (D.B. Baird).
||How to transform the data (
||Maximum number of iterations; default 50|
||Tolerance for convergence; default 0.0001|
||Expression data to be summarized|
||Defines the slides|
||Defines the probes|
||Saves the probe IDs|
||Saves the robust means|
||Saves approximate standard errors of the robust means|
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.
Commands for: Microarray data.
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