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perseus:user:activities:matrixprocessing:outliers:significanceb

Significance B

General

Brief description

Same as Significance A, but intensity-dependent. For details see Cox and Mann (2008) Nat. Biotech. 26, 1367-72.

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

Parameters

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.

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.

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.

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.

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.


Parameter window

Perseus pop-up window: Basic -> Significance B

perseus/user/activities/matrixprocessing/outliers/significanceb.txt · Last modified: 2015/11/23 14:47 (external edit)