StepMiner accepts a PCL file for the time course microarray data. The file format for PCL file is described in Stanford Microarray Database (SMD) at http://smd.stanford.edu/help/formats.shtml#pcl . StepMiner assumes that the arrays are ordered according to the time course. It assigns a number from 0 to (n-1) by default for the time course (n = number of time points). If the headers have a floating point number in them, StepMiner uses them as time points instead of numbers from 0 to (n-1).

For GO Analysis StepMiner requires a gene ontology file in OBO format and a gene annotation file in 15 columns format. In addition to this StepMiner requires the second column of the PCL file describe the gene name. The gene names are matched against the names that are present in the gene annotation file. Therefore, any names that are not present in the gene annotation file are discarded.