GO-Elite Frequently Asked Questions

Warnings and Errors

• GO-Elite returns a warning window while running: WARNING!!!! The length of the input file *input filename* is zero. What's the problem?
• What is the "log" file?

Configuration and Settings

• How can I change the defaults that GO-Elite use?
• Which GO pruning option should I use (z-score, combination, gene-number)?
• How does GO-Elite deal with multiple gene ID mappings?
• How can I add new gene relationships in GO-Elite?
• How to can I update or add new species databases?
• What does 'number changed' and 'number measured' mean in the summary output?
• What is the permutation based p-value?

Analysis

• How can I get all gene associations for a particular GO term not in the pruned list?
• Can I use a list of gene symbols as my input and denominator?
• Can GO-Elite analyze other pathway archives, such as KEGG or Reactome?
• How can I accurately compare GO-Elite results from one input ID list to another?