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Table 4 Comparison of differential gene expression data using Affymetrix one-round and Nugen chemistries.

From: Evaluation of methods for amplification of picogram amounts of total RNA for whole genome expression profiling

Affymetrix

Nugen

status

# probsets

% probsets

status

# probsets

% probsets

D

7423

13.6%

D

3908

52.6%

   

MD

127

1.7%

   

NC

3262

43.9%

   

MI

11

0.1%

   

I

115

1.5%

I

7057

12.9%

D

140

2.0%

   

MD

12

0.2%

   

NC

2996

42.5%

   

MI

118

1.7%

   

I

3791

53.7%

MI

268

0.5%

D

11

4.1%

   

MD

1

0.4%

   

NC

168

62.7%

   

MI

4

1.5%

   

I

84

31.3%

MD

317

0.6%

D

94

29.7%

   

MD

5

1.6%

   

NC

203

64.0%

   

MI

1

0.3%

   

I

14

4.4%

NC

39610

72.4%

D

3358

8.5%

   

MD

268

0.7%

   

NC

32811

82.8%

   

MI

224

0.6%

   

I

2949

7.4%

  1. Targets were generated from RNAs of two cell lines using Affymetrix 1-round IVT and Nugen chemistries. After hybridisation, differential gene expression results were analysed. Status is defined as Decrease (D), Increase (I), Marginal Increase (MI), Marginal Increase (MI), and No Change (NC).
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BMC Genomics

ISSN: 1471-2164

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