Table 2 Quality metrics of gene expression microarray samples

From: Laser capture microdissection enables cellular and molecular studies of tooth root development

Samples

Pos_vs_neg_auca

PM_Meanb

Bgrd_Meanc

Lingual cervical loop

1

0.87

411.74

110.09

 

2

0.85

412.57

121.19

 

3

0.86

542.95

159.21

Apical dental follicle

1

0.87

402.88

114.89

 

2

0.86

390.64

113.54

 

3

0.88

464.59

135.82

Apical dental papilla

1

0.85

363.71

106.72

 

2

0.86

358.40

99.52

 

3

0.86

441.69

125.33

Root odontoblasts

1

0.86

250.25

75.45

 

2

0.85

406.85

104.08

 

3

0.89

234.75

78.08

Root cementoblasts

1

0.86

383.68

107.51

 

2

0.86

351.12

96.45

 

3

0.84

212.35

71.63

  1. a Ratio for detection of positive controls (probes for exons of 100 housekeeping genes) vs. false detection of negative controls (probes for introns of the same 100 housekeeping genes). This metric indicates overall microarray data quality. Typical ratios range between 0.8 and 0.9,with a value of 1.0 being perfect and a value of 0.5 showing no discernable difference between the positive and negative controls. A value significantly below 0.8 strongly indicates poor quality microarray data.
  2. b Mean signal of all perfect match probes (oligonucleotide probes,typically 25-mers containing canonical sequence specific for each gene). These are raw signal intensities before normalization.
  3. c Mean signal of background derived from antigenomic probes,which are designed not to hybridize to any genomic sequence in most studied organisms such as human,mouse,fly and etc. There are about 1000 probes for each level of GC content (0–25).
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