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PCA of data on biomarkers
An example where a 3-d plot is marginally more necessary is given by the biomarker data last see...
Multiple 2-d & 3-d plots
As with MDS, use of Graph>Special>Main>Axes, with (Plot type•2D or •3D), allows any pairs or trip...
Bubble plots on PCA
Of the other options on the Graph>Special menu, overlaying groups from a CLUSTER run (which to be...
Trajectories on PCA
From the Graph>Special menu, remove the vector overlay by unchecking the (✓Overlay vectors) box o...
PCA plot options
Many of the options for manipulating PCA configurations are exactly the same as for MDS plots, co...
PC scores
The final table in the results window is headed Principal Component Scores – these can instead be...
PCA eigen-vector plot
Though the vector overlay has a tendency to clutter the plot, the changing contaminant load along...
Draftsman plots recap & transform choices
Normalisation (subtracting the mean and dividing by the standard deviation, for each variable), a...
Environment-type data
PRIMER uses the term environmental variables as a shorthand for a wide variety of data types (inc...
Tools menu - other items; Tools Options menu
Tools operations on resemblances which are discussed elsewhere are: a) Dissim and Unravel in Sect...
Transform on resemblances; Combining resemblances
Transforming resemblances remains in the Tools menu in PRIMER 7, since it is not an option for pr...
Average body mass matrix (B/A)
A useful variation of this, but one which needs more care, is to compute average body mass of eac...
Expressions combining worksheets
Similarly, expressions can combine samples, or even factors (or indicators) on those samples (or ...
Expressions combining variables
For an example of an Expression combining two (or more) variables, use the Clyde environmental sh...
Transform (individual) advanced
Unlike previous versions, in PRIMER 7 the Transform(individual) routine has been moved to a more ...
Ranked resemblances
Ranking is also a menu option when the active sheet is a resemblance (Tools>Rank distance), but i...
Ranked variables
The following section (on PCA) will discuss further the choice of particular transformations to a...
Missing data estimation (Clyde study)
Transformation options for the Clyde environmental matrix, Clyde environment, are discussed in mo...
EM algorithm assumptions
Tools>Missing is designed to operate only on matrices for which: a) assumptions of multivariate n...
Missing data estimation
The subject of missing data has arisen several times already (Sections 1, 3, 5) and the point mad...