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Table 3 Mutual predictability of the number of barley genes declared differentially expressed from seven data extraction methods.

From: Methods for evaluating gene expression from Affymetrix microarray datasets

Methods AD MAS5.0 MBEI1 MBEI2 RMA PDNN GCRMA
AD 10066 5984(89%) 7951(87%) 8030(93%) 7566(86%) 9269(82%) 6610(90%)
MAS5.0 5984(59%) 6716 5257(57%) 5289(61%) 5614(64%) 6243(55%) 5067(69%)
MBEI1 7951(79%) 5257(78%) 9185 7674(89%) 6969(79%) 8206(72%) 6048(83%)
MBEI2 8030(80%) 5289(79%) 7674(84%) 8650 6744(76%) 7830(69%) 5946(81%)
RMA 7566(75%) 5614(84%) 6969(76%) 6744(78%) 8824 8419(74%) 6736(92%)
PDNN 9269(92%) 6243(93%) 8206(89%) 7830(91%) 8419(91%) 11339 6994(96%)
GCRMA 6610(66%) 5067(75%) 6048(66%) 5946(69%) 6736(76%) 6994(62%) 7310
  1. The diagonal cells show the number of genes declared from each method respectively at FDR = 0.01. The upper and lower triangles show the numbers and percentages (in parentheses) of the genes declared by method j (j = 1st,...,7th column) and also by method i (i = 1st,...,7th row, ij). For example, the 5984 genes in common to AD and MAS5.0 represent 89% of those detected by MAS5.0 but only 59% of those detected by AD.
  2. 1 MBEI PM only model
  3. 2 MBEI PM-MM model