Table 3.

Results of the leave-one-out sensitivity analysis. For each contrast, an individual gene is listed if its removal produced a change in the ranking of the six methodologies. The third column shows how the ranking of the six methodologies changed upon removal of the gene. Here, M = Mas5, G = gcRMA, R = RMA, V = VSN, D = dChip, D- = dChip.mm. Bold font highlights changes. Note that all changes in rankings, with two exceptions, were transpositions of two adjacent methods or a shuffle of three adjacent methods.

CONTRAST	GENE	RANKING
Age	36	(M,D-,G,R,V,D)→(G,M,D-,R,V,D)
Genotype	3	(G,M,D-,R,V,D)→(D-,G,M,R,V,D)
Genotype	12	(G,M,D-,R,V,D)→(M,G,D-,V,R,D)
Genotype	26	(G,M,D-,R,V,D)→(G,M,R,D-,V,D)
Genotype	27	(G,M,D-,R,V,D)→(G,D-,M,R,V,D)
Interaction	4,19	(M,D-,G,R,D,V)→(M,G,D-,R,D,V)
Interaction	6,11,24 27,34,37,43,47	(M,D-,G,R,D,V)→(D-,M,G,R,D,V)
Interaction	8	(M,D-,G,R,D,V)→(M,D-,R,G,D,V)
Interaction	26	(M,D-,G,R,D,V)→(G,M,D-,R,D,V)
Interaction	32	(M,D-,G,R,D,V)→(M,D-,G,R,V,D)
Interaction	12	(M,D-,G,R,D,V)→(G,D-,R,M,V,D)
YWT-OWT	3	(M,G,D,R,V,D-)→(M,G,D,R,D-,V)
YWT-OWT	37	(M,G,D,R,V,D-)→(G,M,D,R,V,D-)
YWT-YMCAT	3	(M,G,D,R,V,D-)→(M,D,G,R,V,D-)
OWT-OMCAT	2,4,8,15,16,20,27,31,34,35,43,47	(D-,G,V,M,R,D)→(D-,G,V,R,M,D)
OWT-OMCAT	10,12,17,18,21,36,39,40,45	(D-,G,V,M,R,D)→(D-,G,M,V,R,D)
OWT-OMCAT	23	(D-,G,V,M,R,D)→(D-,V,G,R,M,D)
OWT-OMCAT	5,6,13,32,33	(D-,G,V,M,R,D)→(D-,G,R,M,V,D)
OWT-OMCAT	3	(D-,G,V,M,R,D)→(D-,M,G,V,R,D)
OWT-OMCAT	26	(D-,G,V,M,R,D)→(G,R,M,V,D-,D)