Significance A


Cox Lab


June 27, 2024

1 General

2 Brief description

Determines which values are significant outliers relative to a certain population. For details see Cox and Mann (Cox and Mann 2008)

Output: A numerical column is added containing the significance A value. Furthermore, a categorical column is added indicating by ‘+’ if a row is significant.

3 Parameters

3.1 Columns

Selected expression columns for which “Significance A” should be calculated (default: no expression columns are selected).

3.2 Side

To apply a two-sided test, where the null hypothesis can be rejected regardless of the direction of the effect “both” has to be selected (default). “left” and “right” are the respective one-sided tests.

3.3 Use for truncation

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

3.4 Threshold value

Based on a specified threshold a specific row is reported as significant (default: 0.05). Depending on the chosen truncation score this threshold value is applied to the p-value or to the Benjamini-Hochberg FDR.

4 Parameter window

Perseus op-up window: Basic -> Significance A


Cox, Jürgen, and Matthias Mann. 2008. “MaxQuant Enables High Peptide Identification Rates, Individualized p.p.b.-Range Mass Accuracies and Proteome-Wide Protein Quantification.” Nature Biotechnology 26 (12): 1367–72.