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Table 2 Chip characteristics of selected data sets studied.

From: G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration

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⟩ 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 probesf

2%

1.9%

2%

2%

2%

%(GGG)1 probesetsf

20%

19%

-

20%

20%

  1. aGene expression omnibus (GEO) accession number
  2. bnumber of probes and of probesets per array
  3. cpseudo sets are assembled using five consecutive probes
  4. dpercentage of absent probes per array
  5. emean value of the logged non specific background intensity and logged saturation intensity
  6. fpercentage of probes containing the (GGG)1-motif and of probe sets containing at minimum one of these probes