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To construct the model, all samples are aligned by a proposed non-rigid dense mesh registration algorithm.
We demonstrate that combining the samples is preferable in that the final model is easier to interpret and generally has smaller uncertainties than the case where we model all samples independently.
Estimated by Bayesian inference using the GTR + Γ model and a fixed clock rate of 0.0105 per lineage/million years, and a coalescent expansion growth model (All samples) or birth-death model (Major clades).
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In total, the correct ratio of the model over all samples is about 438/500 ( (87.60%)).
As the deformable model demands all samples in uniform form, a non-rigid registration algorithm is presented to align the samples in point-to-point correspondence.
The revised Levenberg-Marquardt algorithm in the nonlinear least squares curve fitting can extract the best-fit parameter values in the Adachi's model for all samples.
The PCA model contained all samples and three PCs.
We first fitted an OPLS-DA model of all samples to obtain an overview of genotype-dependent variances.
The overall variation explained by the KED model with all samples is 80%.
In the second step of TileProbe model building, all samples from a given array platform in GEO are grouped according to studies and experimental conditions.
The overall variation explained by the KED model with all samples based on the squared correlation between raw and fitted values is 79%.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com