PCA: Principal Components
Parameter Information
Sample Selection
The sample selection option indicates whether to perform the analysis
on genes or experiments.
Centering Mode
The centering mode selection option determines the type of matrix
centering (by mean, median, or none) to be performed before the PCA analysis is run
Algorithm Optimization
This option determines which algorithm to run when clustering by samples.
The complete algorithm creates an nxn distance matrix where n is the number of genes.
As data sets get large, memory requirements increase exponentially. For most cases, it
is a sufficient approximation to calculate the result using the smaller mxm distance
matrix where m is the number of samples. This dramatically decreases memory requirements
and calculation time.