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In the step estimating marker effects, the estimation of effects of very many markers is hampered by the LD, i.e. collinearity, between the marker effects.
This approach gave early benefits but in later generations, without updating marker effects, the estimation of marker effects based on less related reference individuals did not pay off.
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When re-estimating models based on datasets containing no covariate effect, the estimation of CL was unbiased with all methods, although MIXconc and, to a lesser extent, MIXjoint, overestimated the parameter value.
To provide an impressive stereo effect, the estimation of a background depth profile is necessary.
Such calculations rely on knowledge of the expected variances of the measurements of each group of samples and the magnitude of the treatment effect; the estimation of which is often uninformed and unreliable.
It should be noted that the GEE and random effects models do not estimate the same parameters, since GEE is a marginal model and the random effects allows the estimation of individual effects.
A further problem is potential bias due to epistatic effects in the estimation of additive (e.g. from additive × additive effects) and dominance variance.
More significant effects on the estimation of LD due to sample size are observed for long range LD estimates (marker intervals greater than 10 kb).
In this work, we considered an additive polygenic effect in the estimation of marker effects but it may not completely correct for stratification.
Effects on the estimation of prevalence may be of importance as well.
A potential limitation of working with grouped data is in the identification of fixed effects in the estimation of Eqs.
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