## 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]
- Which mean to use (geometric, arithmetic) [geometric]
- Scale (log2, linear) [log2]

### Details

User needs to select a phenodata column that defines the grouping of the samples. Mark both groups in the phenodata file with numbers, and use smaller number for the control/baseline group. So for example control samples can be coded with "1" and treatment samples with "2" in the group column. Then Chipster knows to compare treatment to control (control is coded with a smaller number than the treatment). Since this makes a difference when interpreting the results such as fold change, it is worth paying attention to.

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.