• For custom spotted arrays, the quantity used for analysis is most often the

\[log_2(\frac{SampleSignal}{ReferenceSignal})\]

• This ratio may or may not include background subtraction

\[log_2(\frac{SampleSignal-SampleBackground}{ReferenceSignal-ReferenceBackground})\]

• Fold changes, or ratios, can be larger than 1 (2-fold increase), or smaller than one (0.5).
• Not symmetric around 1

• \(log_2(\frac{x}{y}) = log_2(x)-log_2(y)\) - fold change converted to difference
• log ratios are symmetric around 0
• \(log_2(1) = 0\)
• \(log_2(2) = 1\)
• \(log_2(0.5) = -1\)

• Note that on a log scale,
• The differences are 1.

• The fold change distribution has a fat right tail
• The log2-transformed fold changes are linear