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, 17:40, 11 October 2012
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| Firth test is relatively computationally intensive compared to the score test. However, Firth has better test properties (i.e. type I error rates and power) compare to score test when analyzing low frequency variants in studies with unequal numbers of cases and controls. | | Firth test is relatively computationally intensive compared to the score test. However, Firth has better test properties (i.e. type I error rates and power) compare to score test when analyzing low frequency variants in studies with unequal numbers of cases and controls. |
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− | For example, using 1 CPU, analyzing 2333 FUSION individuals, chromosome 20, 22755 SNPs (adjusting for age, sex and 11 dummy variables for birth province): | + | For example, using a single CPU, analyzing 2333 FUSION individuals, chromosome 20, 22755 SNPs (adjusting for age, sex and 11 dummy variables for birth province): |
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− | *Firth test: 56 minutes (3360 seconds) | + | *Firth test: 56 minutes (3360 seconds) |
| *Score test: 32 seconds | | *Score test: 32 seconds |
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− | <br> This is the reason why we only ask for Firth test results for SNPs with MAC <= 200. | + | <br> Hence, we only ask for Firth test results for SNPs with MAC <= 200. |
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| === 1. Typical DIAGRAM analysis using existing association pipeline<br> === | | === 1. Typical DIAGRAM analysis using existing association pipeline<br> === |