What is the difference between the Smallest Category Size for Category Statistics and the Largest Category Size to Include in CIM?
The Smallest Category Size for Category Statistics parameter is broader. It is used in all variants of GoMiner. Categories whose size is less than this threshold will be omitted from category statistic calculations. Many reports and displays will still include these categories, but they won’t have p-values, enrichment ratios, or FDR’s. This threshold is also used to filter smaller randomized categories when determining the FDR. The Largest Category Size to Include in CIM has a more limited scope. It only affects the CIM’s, a report-type in HTGM. It eliminates the categories above the threshold from the category gene matrixes.
