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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, i≠j). 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