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    %% Normalize Affymetrix data 
% This example shows how to normalize affymetrix data. The
% |prostatecancerrawdata.mat| file used in the example contains data from
% Best et al., 2005.

% Copyright 2015 The MathWorks, Inc.


%%
% Load a MAT-file, included with the Bioinformatics Toolbox(TM) software,
% which contains Affymetrix data variables, including |pmMatrix| , a matrix of
% PM probe intensity values from multiple CEL files.
load prostatecancerrawdata

%%
% Normalize the data in pmMatrix and plot data from columns (chips) 2 and
% 3. Column 1 is the baseline.
NormMatrix = affyinvarsetnorm(pmMatrix, 'Showplot',[2 3]);

%%
%