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perseus:user:activities:matrixprocessing:annotcolumns:fisherexacttestproces

Fisher exact test

General

Brief description

This is a test used to determine if there are non-random associations between a categorical column and all terms in the other categorical columns. Note that significantly enriched as well as depleted terms will be reported. Depleted terms will have an enrichemnt factor < 1.

Output: A new table is generated in which each row corresponds to a term in a categorical column that is significantly associated with a term in the selected categorical column.

Parameters

Input type

Specification whether the sub-population that is tested for contingency against all other categorical columns is taken directly from a categorical column (“Categorical column” is default) or, if it is defined by a threshold on a numerical/expression column (“Numerical column”).

Column

This parameter is just relevant, if “Input type” is set to “Categorical column”. The selected categorical column is checked against all other categorical columns for association between the occurrence of terms (default: first categorical column in the matrix).

Columns

This parameter is just relevant, if “Input type” is set to “Numerical column”. The selected expression/numerical columns are used for thresholding to define the set of interest. The set is then checked against all categorical columns for association between the occurrence of terms (default: all expression and numerical columns are selected).

Threshold

This parameter is just relevant, if “Input type” is set to “Numerical column”. It defines the threshold, which rows are kept/discarded to define the set of interest (default: 2).

Selection is

This parameter is just relevant, if “Input type” is set to “Numerical column”. It defines, whether the values in the selected “Columns” should be “Larger than threshold” or “Less than threshold” (default: Larger than threshold).


Use for truncation

The truncation can be based on p-values or the Benjamini-Hochberg correction for multiple hypothesis testing (default: Benjamini-Hochberg FDRFalse Discovery Rate). Rows with a test result below a specified value (parameter below) are reported as significant.

Threshold value

Based on a specified threshold (default: 0.02) a specific row is reported as significant. Depending on the chosen truncation score (parameter above) this threshold value is applied to the p-value or to the Benjamini-Hochberg FDR.

Relative enrichment

Selected text column, where all rows having the same identifier will be counted as one entity in the Fisher exact test (default: <None>). The main application is for posttranslational modification sites. Then one should select here protein or gene identifiers. This will make sure that multiple sites from the same protein (or gene) are counted only once for the enrichment analysis.


Parameter window

Perseus pop-up window: Annot. columns -> Fisher exact

perseus/user/activities/matrixprocessing/annotcolumns/fisherexacttestproces.txt · Last modified: 2015/12/09 16:33 by temu