Method

AD

MAS5.0

MBEI^{1}

MBEI^{2}

RMA

GCRMA

PDNN


AD

0.991 ± 0.005

0.975 ± 0.004

0.988 ± 0.001

0.985 ± 0.001

0.647 ± 0.007

0.791 ± 0.008

0.615 ± 0.007

MAS5.0

0.973

0.984 ± 0.009

0.961 ± 0.005

0.965 ± 0.003

0.619 ± 0.026

0.748 ± 0.024

0.583 ± 0.026

MBEI^{1}

0.987

0.958

0.990 ± 0.005

0.988 ± 0.001

0.664 ± 0.011

0.797 ± 0.009

0.629 ± 0.008

MBEI^{2}

0.985

0.963

0.988

0.990 ± 0.005

0.643 ± 0.006

0.774 ± 0.006

0.605 ± 0.006

RMA

0.647

0.616

0.662

0.643

0.993 ± 0.003

0.914 ± 0.002

0.939 ± 0.008

GCRMA

0.791

0.744

0.797

0.774

0.914

0.992 ± 0.005

0.923 ± 0.004

PDNN

0.614

0.581

0.628

0.604

0.940

0.923

0.992 ± 0.005

 The upper triangle shows the mean and corresponding standard deviation of 24 correlation coefficients, r_{
ijk
}, (k = 1, 2,..., 24). r_{
ijk
}represents the correlation coefficient between 22,840 corresponding pairs of gene expression indices calculated by methods i and j from the k^{th} microarray sample. The diagonal cells show means and standard deviations of 24 correlation coefficients, r_{
imn
}(n = 1, 2, 3 and m = 1, 2,..., 8). For n = 1, 2, 3, r_{
imn
}corresponds to three correlation coefficients calculated from three possible pairs of replicates for the m^{th} cultivar (m = 1, 2,..., 8) using method i. The lower triangle shows the correlation coefficients between all pairs of 22,840 gene expression indices calculated from methods i and j across all k = 24 samples.
 ^{1} MBEI PM only model
 ^{2} MBEI PMMM model