Significance B

Author

Cox Lab

Published

March 18, 2024

1 General

2 Brief description

Same as Significance A, but intensity-dependent. For details see Cox and Mann (2008) (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 Ratio columns

Selected expression columns containing the ratios for which “Significance B” should be calculated (default: no columns are selected).

Hint: The number of selected ratio columns must be the same as the number of selected intensity columns.

3.2 Intensity columns

Selected expression/numerical columns containing the intensities for which “Significance B” should be calculated (default: no columns are selected).

Hint: The number of selected intensity columns must be the same as the number of selected ratio columns.

3.3 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.

3.3.1 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 pop-up window: Basic -> Significance B

References

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. https://doi.org/10.1038/nbt.1511.