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Table 2 Pearson's Product Moment Correlation Coefficients among barley gene expression indices calculated from seven different methods.

From: Methods for evaluating gene expression from Affymetrix microarray datasets

Method AD MAS5.0 MBEI1 MBEI2 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
MBEI1 0.987 0.958 0.990 ± 0.005 0.988 ± 0.001 0.664 ± 0.011 0.797 ± 0.009 0.629 ± 0.008
MBEI2 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
  1. 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 kth 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 mth 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.
  2. 1 MBEI PM only model
  3. 2 MBEI PM-MM model