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Given that all the sub-components are either dichotomous or ordinal, I perform a principle component analysis using a polychoric correlation matrix.
We also perform a principle coordinate analysis using the distance matrices and plot the samples on the first two principle coordinates (Fig. 5).
The SNPRelate package (Zheng et al. 2012) was used to perform a principle component analysis, and eigenvalue1 and eigenvalue2 were used to visualize samples.
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The WGCNA further performs a principle component analysis (Pearson 1901; Hotelling 1933; Zhang and Horvath 2005) on the expression matrix of each gene module and uses the first principle component (designated as "Eigen gene") as the representative of the gene module.
As a final quality control step we performed a principle component analysis and plotted the first two principle components to show that replicated samples were grouping together.
To determine whether the group was homogeneous or whether different types of variation were represented, we performed a Principle Components Analysis (PCA).
Step 9, performing a principle component analysis (PCA), can be done using Matlab software (Mathworks, Natwich, MA) or similar statistical software.
Performing a Principle Components Analysis (PCA) to visualize the data, a negative correlation between the sugars with the greatest influence on data variability (those with the longest vector, namely erlose, glucose, and fructose) could be observed.
Since multiple cluster 1 measures and UAW were found to be associated with similar sets of SNP markers, we performed a principle component analysis (PCA) to evaluate whether some "lower-dimensional summary" of these variables provide more information about the observed associations.
For a broad scale examination of variation, we performed a principle components analysis of all samples.
A formal test of the assumption of unidimensionality is undertaken by performing a principle component analysis (PCA) of the residuals.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com