What is Fold Change
From Array Suite Wiki
Many users are more comfortable dealing on a linearscale, rather than a log scale.
A Fold Change, as defined by many users, and Omicsoft, is the unlogged estimate. So, on a log scale of 2, if the estimate is 2, then the Fold Change is 2^2 or 4. If the estimate is -2, then the fold change is -(2^abs(-2)), or -4. A fold change can have a range of (1, infinity) and (-infinity, -1) but cannot have a value between -1 and 1.
If the original data had been on a linear scale, this would be the equivalent of taking the geometric mean of Treatment/geometric mean of Control. Consider the following example: On a linear scale the expression values are 16, 32, and 64 for the Treatment (equivalent to 4,5, and 6 on a log-2 scale), and 4, 8, and 16 for control (equivalent to 2,3, and 4 on a log-2 scale). So, the geometric mean of the treatment group would be 32, while the geometric mean of the control group would be 8. Thus, if you take 32/8, you get a fold change of 4 (equivalent to the estimate generated above). Some other programs, when generating fold changes, use the average (or arithmetic mean) to generate their fold change values, using a linear scale. (This would be Average of Group A/Average of Group B). However, statisticians agree that it is more appropriate to use the geometric mean (linear scale) or arithmetic mean (log scale), so that is what Array Studio does to generate fold changes.
A positive fold change indicates that the first group in a contrast is upregulated compared to the second group.
A negative fold change indicates that the first group in a contrast is downregulated compared to the second group.