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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.