Model Definition File: This is a tab-delimited file containing the user-defined model patterns. The model patterns can be prepared in Excel and saved as a tab-delimited text file. One row represents a single model pattern. The first field of each row must provide the pattern name and the subsequent fields should be numerical values that define the pattern. The number of data points in each pattern must be the same as the number of data points in the experimental data file.

Example:

pattern_1	1	0.5	0.25	0.1	0.1	0.1

Experimental Data File: This is a tab-delimited file containing the data to be analyzed. Typically this file contains unlogged microarray expression values. The first field of each row must provide a name defining that row. Typically this is a gene or microarray probeset identifier. The subsequent fields within a row contain the expression values. The number of data points in each row of data must be the same as the number of data points in the model pattern file.

Example:

Gene_1	100.1	207.9	259.9	992.3	887.2	913.6

Correlation Cutoff: This is the threshold for the Pearson's correlation coefficient derived by comparison of the model and experimental data series.

Fold Cutoff: This threshold determines the minimum acceptable fold-difference (i.e., max/min) between the maximum and minimum values in the data series.

P-value Cutoff: This is the significance threshold for the one-tailed p-value calculated for the Pearson’s correlation coefficient.

Background Cutoff: This is the minimum acceptable value for the highest value in the series. This cutoff is useful to prevent spurious model/data matches involving data series in which all of the data points are all below the background level (i.e., noise) in your experiment.