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Table 4 Effects of low expressed gene elimination on SFP detection performances in transcript hybridization by SNEP.

From: A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays

Tissue type

Shoot

Expressed

Shoot All

Young panicle All

Young panicle All

Total probe sets

12,620

41,525

12,538

41,525

Total probes

121,763

391,818

120,708

391,818

SFP probes

6,657

58,150

6,549

58,150

SNEP threshold

10-6.0

10-6.0

10-11.25

10-6

10-6.0

10-10.05

Called

4,324

7,793

5,136

4,467

7,492

5,727

TRUE

3,393

5,442

4,030

3,513

5,440

4,502

 

51.0%

9.4%

6.9%

53.6%

9.4%

7.7%

FALSE

931

2,351

1,106

954

2,092

1,225

 

21.5%

30.2%

21.5%

21.4%

27.4%

21.4%

  1. Numbers of "Shoot Expressed" and "Young panicle Expressed" were from Table 3. Numbers of SNEP analyses for "all" were summarized both at the same SNEP threshold, 10-6, and at the same FPR of "Expressed".
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BMC Genomics

ISSN: 1471-2164

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