# Single-, two-, multi-class SAM

These SAM versions are extensions of

## Single Class SAM

In this version of SAM genes are searched which show clear
regulation throughout all selected hybridisdations.

Basic test statistic is a **single class T-test**.

### Parameters:

- One group of hybridisations has to be defined
- Number of permutations
- How to find s
_{0} (fudge factor)
- Delta

### Results:

- Delta table
- Values for selected Delta
- List of up-regulated significant genes
- List of down-upregulated significant genes
- List of regulated significant genes
- List of non-regulated significant genes

### Gene lists may be visualised and saved as

- genelist with basic statistical values
- sub-expression matrices
- expression profiles
- centroid graphs
- heatmaps

## Two class SAM

In this version of SAM genes are searched which can
distinguish between two groups of hybridisations (e.g. cancer <=> normal).

Basic test statistic is a **two class T-test**.

### Parameters:

- Two groups of hybridisations have to be defined
- Number of permutations
- Permutation balancing
- How to find s
_{0} (fudge factor)
- Delta

### Results:

- Delta table
- Values for selected Delta
- List of up-regulated significant genes
- List of down-upregulated significant genes
- List of regulated significant genes
- List of non-regulated significant genes

### Gene lists may be visualised and saved as

- genelist with basic statistical values
- sub-expression matrices
- expression profiles
- centroid graphs
- heatmaps

## Multi class SAM

In this version of SAM genes are searched which can
distinguish between three or more sub-groups of hybridisations

(e.g. kidney <=> liver <=> pancreas <=> lung <=> brain <=> ...).

The present version can handle a maximum of 12 independant groups.

Basic test statistic is **ANOVA**

### Parameters:

- Three or more groups of hybridisations have to be defined
- Number of permutations
- Permutation balancing
- How to find s
_{0} (fudge factor)
- Delta

### Results:

- Delta table
- Values for selected Delta
- List of up-regulated significant genes
- List of down-upregulated significant genes
- List of regulated significant genes
- List of non-regulated significant genes

### Gene lists may be visualised and saved as

- genelist with basic statistical values
- sub-expression matrices
- expression profiles
- centroid graphs
- heatmaps

In the SAM graph you find only the upper right quadrant (both x-
/ and y-axis have only positive values).

Also, you only find selections for positive significant and non significant
genes.

last edited 26.04.2006