From: Genotyping and inflated type I error rate in genome-wide association case/control studies
Name | Summary Statistic | MM1 | Data2 | Data3 | Notes |
---|---|---|---|---|---|
RLMM | {Θ A , Θ B } | No | T | M |  |
BRLMM |
| No | E-U | M | Assumes genotypes in "training" data are known. "Training" data only uses high quality SNPs. Incorporates info from other SNPs as a B ayesian Prior. |
CRLMM | {ΘA+- ΘB+, ΘA-- ΘB-} | No | T | L | C orrects for the effect of total intensity level and probe length on {S ij } through more complex method, and allows corrections to vary by array. |
CHIAMO |
| Yes | E-L, T* | W | CHIAMO is a Bayesian hierarchical mixture model and is greatly simplified by this brief summary |
SNiPer-HD |
| No | E-U | W | Assumes genotypes in "training" data are unknown and requires the EM algorithm. "Training" data should only use high quality SNPs. |
Moorhead |
| N/A | E-U | W | Originally for MIP, but applicable to Affymetrix. Plagnol demonstrated how to link genotype probabilities between cases and controls. |
logiCALL |
| No | E-L | W-F | Designed to lower false positive rate and assigns calls based on cumulative distribution, not density functions. |