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GREAT currently supports test files with up to 500,000 test regions and background files with up to 1,000,000 regions. Each must be less than 20 50 MB in size. Compressed data must decompress to plain text files at most 50 MB in size.

GREAT version 1.2 supported at most 200,000 test regions and did not support compressed data as input.

Handling large data sets

By default GREAT displays data in a "Significant by Both" View that only shows terms significant by both the binomial test over genomic regions and the hypergeometric test over genes. Large data sets can cause a large fraction of all genes to be selected via the regulatory domain association rules. This often results in saturation of the hypergeometric test over genes such that no hypergeometric test results are significant. The binomial test over genomic regions is robust to large data sets, however.