Table 1

As the threshold stringency increases, the number of known imprinted genes identified as differentially expressed at a q < 0.05 reaches a local optimum while the number of significant genes decreases.

Effects of filtering at various thresholds on the Affymetrix Human array


Filter Thresholds

PM Threshold

Number of Probes After Filtering

% Probes After Filtering

% Probe Sets Remaining

Number Significant (q < 0.05)

Number Known Imprinted (q < 0.05)

Number Significant (padj< 0.05)

Number Known Imprinted (padj< 0.05)


No filter

0.000

604,258

100.0%

100.00%

21

4

8

2

Median

7.655

361,110

59.8%

99.11%

20

6

7

2

75% quartile

8.479

197,484

32.7%

92.80%

14

6

4

2

1 standard deviation above mean

9.104

113,455

18.8%

79.20%

6

3

3

2


Tsai et al. BMC Genomics 2006 7:328   doi:10.1186/1471-2164-7-328

Open Data