Table 2

Chip characteristics of selected data sets studied.

Data Set

HG133A_S

Mouse

ENCODE

HG133P_Z

HG133A_Z

GEO^a

GSE1133

GSE12545

GSE6292

GSE3061

GSE3061

Chip type

HG U133A

MG 430 2.0

Human Tiling

HG U133plus2

HG U133A

# probes × 10^{6 b}

≈ 0.5

≈ 1.0

≈ 1.5

≈ 1.2

≈ 0.5

# probesets^b

22,300

45,101

300, 000^c

54,675

22,300

% absent^d

61.9%

63.1%

94.8%

54.9%

42.8

⟨ log L^N⟩_chip^e

2.0

2.3

1.1

1.94

2.09

log I_max^e

4.48

4.71

3.45

4.32

4.45

%(GGG)₁ probes^f

2%

1.9%

2%

2%

2%

%(GGG)₁ probesets^f

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

Fasold et al. BMC Bioinformatics 2010 11:207   doi:10.1186/1471-2105-11-207