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Analyses of the two simulated datasets with this new method showed that 1) the parameters involved in adjusting marker-based and pedigree-based relationship matrices can depend on both observed phenotypes and observed marker genotypes and 2) a strong association between these two parameters exists.
CheckMatrix heat plots were used to visually inspect and adjust marker grouping and order.
One advantage of 2b-RAD methodology is the option to adjust marker density to the desired level using selective adaptors.
Like 2b-RAD, SLAF-seq can also adjust marker identification and genotyping to meet personalized research purposes.
The Bonferroni Holm procedure [ 74] was used to adjust marker-trait associations for multiple testing.
Adjusting for marker polymorphism by calculating Hedrick's GST [28] did not change any of the above conclusions (e.g., more than half of the pair-wise FST values were negative).
This phenomenon was attributed to fluctuations in the baseline of sequence traces and was corrected by proportionally adjusting all marker frequencies to give a total of 100% (Table 3).
Finally, this method performed at least as well as a method based on adjusting the marker-based relationship matrix.
Some investigations have demonstrated that PAI-1 is predictive of T2DM but that its predictive ability disappears after adjusting for markers of metabolic syndrome [ 15, 16].
PBMC CD36 protein, but not CD36 mRNA, levels remained higher among patients with type 2 diabetes versus control subjects, after adjusting for markers of inflammation, blood pressure, and insulin sensitivity.
We dealt with confounding by indication by restricting the analysis to patients with very severe oxygen dependent COPD and by adjusting for markers of the severity of underlying disease, comorbidity, and concomitant drug treatments.
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