Sidebar
perseus:user:activities:matrixprocessing:outliers:significanceb
Table of Contents
Significance B
General
- Type: Matrix Processing
- Heading: Outliers
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 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 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/user/activities/matrixprocessing/outliers/significanceb.txt · Last modified: 2015/11/23 14:47 (external edit)
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution 4.0 International
