Date help created: 25 Sep 2000 Date last updated: 25 Sep 2000'components' calculates the principal components of a group of spectra. The pseudo-spectra, which are the linear combinations of the spectra as determined by the compnents, can be output, as well as the weights of each spectrum relative to the components.
The input data files must not be deflated.
To run the program type
components <components script file>
The components script file must have the following format:
input_list <file containing list of input par files> output_data <prefix for output pseudo-spectra> ! optional output_weights <output weights file> ! optional components <minimum number of components to calculate> ! optional fraction <minimum fraction of weight to calculate> ! optional correlation ! optional
One or both of 'output_data' and 'output_weights' must be given.
The input list file must have just a list of files, one per line.
The minimum number of components calculated is 1/10 the number of input files if 'components' does not appear.
The minimum fraction of weight (the sum of the eigenvalues) calculated is 0.95 if 'fraction' does not appear.
If 'correlation' appears the correlation matrix is used to calculate the principal components, otherwise the covariance matrix is used. The correlation matrix is basically the normalised covariance matrix. In general, it is probably best to use the covariance matrix.
The following is an example script file:
input_list 84list.txt output_data 84pca.spc output_weights 84weights.txt components 4 fraction 0.9
with 84list.txt being:
841.spc.par 842.spc.par 843.spc.par 844.spc.par 845.spc.par 846.spc.par 847.spc.par 848.spc.par
Assuming the first 4 components are sufficient to give 0.9 of the total weight then the following files are created because of the 'output_data' statement:
84pca.spc1 84pca.spc2 84pca.spc3 84pca.spc4
The corresponding par files are also created:
84pca.spc1.par 84pca.spc2.par 84pca.spc3.par 84pca.spc4.par Azara help: components / W. Boucher / azara@bioc.cam.ac.uk