www.gusucode.com > bioinfo 案例源码程序 matlab代码 > bioinfo/CalculateAffymetrixProbeAffinitiesExample.m

    %% Calculate Affymetrix probe affinities
% This example shows how to calculate Affymetrix PM and MM probe affinities
% from their sequences and MM probe intensities.

% Copyright 2015 The MathWorks, Inc.


%%
% Load the MAT-file, included with the Bioinformatics Toolbox(TM) software,
% that contains Affymetrix data from a prostate cancer study. The variables
% in the MAT-file include |seqMatrix| , a matrix containing sequence
% information for PM probes, |mmMatrix| , a matrix containing MM probe
% intensity values, and |probeIndices| , a column vector containing probe
% indexing information.
load prostatecancerrawdata

%%
% Compute the Affymetrix PM and MM probe affinities from their sequences
% and MM probe intensities, and also plot the affinity values of each of
% the four bases (A, C, G, and T) for each of the 25 sequence positions,
% for all probes on the Affymetrix GeneChip array.
[apm, amm] = affyprobeaffinities(seqMatrix, mmMatrix(:,1),...
             'ProbeIndices', probeIndices, 'showplot', true);
%%
% The prostatecancerrawdata.mat file used in this example contains data
% from Best et al., 2005.