## Utilities / Calculate fold change

### Description

Calculates a geometric or arithmetic average of gene expression for replicate chips and then calculates a difference or ratio between the averages. This tool is applicable only if the data has two groups.

### Parameters

- Column [group]
- Geometric (yes, no) [yes]
- Scale (log2, linear) [log2]
- Order (normal, reverse) [normal]

### Details

User needs to select a phenodata column that defines the grouping of the samples. The reference group selection is controlled by the "order" parameter: In the normal mode the group of the first sample is assumed to be the reference, whereas in the reversed mode the situation is reversed. Note that this is different to how # FC values are calculated in the various statistical testing tool, where the reference group is defined by the lower group number or alphabetical order.

First the samples in both groups are averaged - either using the geometric or arithmetic mean - and then a fold change of these averages is calculated. In most cases the geometric mean is considered the most appropriate way to calculate the average expression, especially for data from 2-color array experiments. Fold change is reported in either linear or base 2 logarithmic scale. By default, the output is given in base 2 logarithmic scale, due to the statistical benefits and the ease of use and graphical interpretation this brings. However, sometimes users may wish to report the fold changes as linear ratios, which can be achieved by setting the "scale" parameter accordingly.

### Output

A table with the fold change values.