Table 2.

Chip characteristics of selected data sets studied.

Data Set	HG133A_S	Mouse	ENCODE	HG133P_Z	HG133A_Z
GEOa	GSE1133	GSE12545	GSE6292	GSE3061	GSE3061
Chip type	HG U133A	MG 430 2.0	Human Tiling	HG U133plus2	HG U133A
# probes × 106 b	≈ 0.5	≈ 1.0	≈ 1.5	≈ 1.2	≈ 0.5
# probesetsb	22,300	45,101	300, 000c	54,675	22,300
% absentd	61.9%	63.1%	94.8%	54.9%	42.8
⟨ log LN⟩chipe	2.0	2.3	1.1	1.94	2.09
log Imaxe	4.48	4.71	3.45	4.32	4.45
%(GGG)1 probesf	2%	1.9%	2%	2%	2%
%(GGG)1 probesetsf	20%	19%	-	20%	20%

^a Gene expression omnibus (GEO) accession number

^b number of probes and of probesets per array

^c pseudo sets are assembled using five consecutive probes

^d percentage of absent probes per array

^e mean value of the logged non specific background intensity and logged saturation intensity

^f percentage of probes containing the (GGG)₁-motif and of probe sets containing at minimum one of these probes