Number of components

This parameter is just relevant, if the parameter “Category enrichment in components” is checked. It specifies the number of principal components that will be used for the transformation (default: 5).

Cutoff method

This parameter is just relevant, if the parameter “Category enrichment in components” is checked. It defines the method that is used to calculate the cutoff of potential principal components (default: Benjamini-Hochberg FDRFalse Discovery Rate) . The method can be selected from a predefined list:

• Benjamini-Hochberg FDR
• p-value

Threshold

This parameter is just relevant, if the parameter “Category enrichment in components” is checked. It defines the threshold value of the previously specified used cutoff method (default: 0.05).

Relative enrichment

This parameter is just relevant, if the parameter “Category enrichment in components” is checked. It defines, which categorical column will be used to group rows in the enrichment test (default: <None>). All rows having the same identifier will be counted as one entity in the enrichment test. 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.