Tech Notes

Q. How does the Filter on Fold Change calculate fold changes in log mode and is it appropriate?

The Filter on Fold Change feature allows you to filter genes based on the fold change between two conditions. The fold change for each gene is calculated as the average expression over all samples in Condition 1 divided by the average expression over all samples in Condition 2. If Normalized Data is chosen as the data type, the calculation of these averages depends on the interpretation mode. If the interpretation is in Ratio mode, the average within each condition will be calculated using the arithmetic mean of the normalized ratios; these means are then used to construct the fold change ratio.

If the interpretation is set to Log of ratio mode, the geometric mean of the normalized ratios within each condition is used to calculate fold-change ratio. The geometric mean is calculated by taking the nth root of the product of the n normalized ratios within a condition. Equivalently, it is the anti-logarithm of the arithmetic mean of the logged ratios. It is generally accepted that using log mode to perform such analysis is appropriate.

The geometric mean is sometimes used in averaging ratios as it gives each ratio equal weight (1). It is used in conjunction with Log of ratio mode, as it equalizes the contribution of ratios representing both up- and down-regulation. In addition to ratio and log mode, a "fold-change" mode is available. This is the least conventional method of applying fold-change, as it will give distinct results from the other two modes. It is therefore not the recommended interpretation mode for Filter on Fold Change.

Ultimately, the choice of mode over which to apply the Filter on Fold Change is a matter of preference. As GeneSpring uses the log of ratio mode in the default interpretation, change the interpretation mode to "Ratio (Signal/Control)" if you wish to use the arithmetic mean in your fold change analysis.

(1) Zar, J.H. 1999. Biostatistical Analysis. 4th ed. Prentice Hall, Upper Saddle River, New Jersey.