Table 1.

Pairwise Comparisons

POTATO	NLA	NLC	NVA	NVC	HLA	HLC	HVA	HVC
NLA	100	69	74	65	77	67	63	55
NLC		100	61	69	63	84	52	62
NVA			100	77	66	60	79	66
NVC				100	58	67	67	82
HLA					100	71	70	60
HLC						100	58	74
HVA							100	72
HVC								100

GRAPEVINE	NL	NV	HL	HV	SL	SV	NeL	NeV
NL	100	67	67	67	67	66	70	66
NV		100	79	89	78	89	88	89
HL			100	83	95	83	86	83
HV				100	82	92	89	92
SL					100	82	84	82
SV						100	91	100
NeL							100	91
NeV								100

MOUSE	NL	NV	HL	HV	SL	SV	NeL	NeV
NL	100	80	65	73	69	74	83	71
NV		100	63	83	70	84	64	79
HL			100	66	83	68	66	69
HV				100	75	92	64	87
SL					100	75	67	78
SV						100	68	85
NeL							100
NeV								100

Pairwise comparisons of the number of genes, present in the top 100 genes list that showed evidence for differential expression under different data analysis conditions. Combinations of all background correction (N—none, H—half and for grapevine, also S—subtract and Ne—normexp), normalization (L—loess, V—vsn) and spot averaging for potato (A—average, C—duplicate correlation) that was done are shown.