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==== Parameters: ====

* '''Experiment''' - experimental data for analysis.
** '''Table''' - a table data collection with experimental data stored in the BioUML repository.
** '''Columns''' - the columns from the table which should be taken into account.
* '''Control''' - control data for analysis (not obligatory).
** '''Table''' - a table data collection with control data stored in the BioUML repository.
** '''Columns''' - the columns from the table which should be taken into account.
* '''Output type''' - the type of genes to be included in the result table:
** Up- and down-regulated
** Up-regulated
** Down-regulated
* '''''P-value'' threshold''' - the threshold for the ''P-value'' (only genes with lower ''P-value'' will be included in the results)
* '''Outline boundaries''' - lower and upper boundaries for values from the input table. Outliers will be ignored.
* '''Boundary value''' - an expression will be compared with that value. If you want to compare experimental data with control you should set it equal to 1.
* '''Calculate FDR''' - the test method for calculation of False Discovery Rate (FDR) - an average rate of mistakenly found up or down regulated genes with a given ''P-value'' threshold. It random permutates the data 50 times and applies hypergemetric test to each randomized set. FDR is calculated separately for up and down regulated genes according to the formula:
*::: [[File:Statistics-Hypergeometric-analysis-fdr.png]]
* '''Detailed output''' - whether some technical information will be included in result or not.
* '''Output table''' - the path in BioUML repository where the result table will be stored. If a table with the specified path already exists it will be replaced.