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multiplesampletestprocessing.qmd
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multiplesampletestprocessing.qmd
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---
title: "Multiple-samples tests"
author: "Cox Lab"
format:
html:
toc: true
toc-depth: 4
toc-expand: false
number-sections: true
number-depth: 4
editor: source
date: today
bibliography: references.bib
---
# General
- **Type:** - Matrix Processing
- **Heading:** - Tests
- **Source code:** not public.
# Brief description
Multi-sample test for determining if any of the means of several groups is significantly different from each other.
Output: A numerical columns is added containing the p-value. In addition there is a categorical column added in which it is indicated by a '+' when the row is significant with respect to the specified criteria.
```{=html}
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The recommended sections are these, but they may be changed on a case by case basis.
===== Detailed description =====
===== Parameters =====
===== Theoretical background =====
===== Examples =====
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```
# Parameters
## Grouping
Selected categorical row that defines the grouping of columns that should be used in the test (default: first categorical row in the matrix).
## Test
Defines what kind of test should be applied (default: ANOVA). The test can be selected from a predefined list:
- ANOVA
- Kruskal Wallis
### S0
Artificial within groups variance (default: 0). It controls the relative importance of t-test p-value and difference between means. At $s0=0$ only the p-value matters, while at nonzero s0 also the difference of means plays a role. See [@tusher2001] for details.
## Use for truncation
Defines on what value the truncation is based on (default: Permutation-based FDR). Choose here whether the truncation should be based on the p-values, on permutation-based FDR-values or, if the Benjamini-Hochberg correction for multiple hypothesis testing should be applied.
### Threshold p-value
This parameter is just relevant, if the parameter "Use for truncation" is set to "P-value". Rows with a test result below this value are reported as significant (default: 0.05).
### FDR
This parameter is just relevant, if the parameter "Use for truncation" is set to "Benjamini-Hochberg FDR" or "Permutation-based FDR". Rows with a test result below this value are reported as significant (default: 0.05).
### Number of randomizations
Specifies the number of randomizations that should be applied (default: 250).
### Preserve grouping in randomizations
Defines, whether the grouping specified in a categorical row should be preserved in the randomizations (default: `<None>`). It can be selected from a list including all available groupings of the matrix.
## Log10
If checked, $-Log_{10}(test\ value)$ is reported in the output matrix (default). Otherwise the test-value is reported.
## Suffix
The entered suffix will be attached to newly generated columns (default: empty). That way columns from multiple runs of the test can be distinguished more easily.
# Parameter window
