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Table 3 The percentage of 'p-values' less than traditionalα-levels (0.005,0.001,0.005) are listed for four tests of association.

From: Genotyping and inflated type I error rate in genome-wide association case/control studies

Method

n

p < 0.005

p < 0.001

p < 0.0005

BeadStudio

3487

0.015

0.005

0.004

logiCALL

5533

0.004

0.002

0.002

LR

5533

0.087

0.061

0.052

LR-(same)

3014

0.006

0.002

0.001

  1. 1) BeadStudio (default setting for missing assignements and omitting SNPs).
  2. 2) logiCALL.
  3. 3) Likelihood Ratio (LR) using all SNP.
  4. 4) Likelihood ratio (LR-same) using only SNP where calls were the same for restricted and unrestricted parameter sets.