What is the objective of Transformation and which transformation method should be used for expression ratios?
A. The expression ratio is a relevant way of representing expression differences in a very intuitive manner. For example, genes that do not differ in their expression level will have an expression ratio of 1. However, this representation may be unhelpful when one has to represent up-regulation and down-regulation. For example, a gene that is up-regulated by a factor of 4 has an expression ratio of 4 (R/G = 4G/G = 4). However, for the case where a gene is down regulated by a factor of 4, the expression ratio becomes 0.25 (R/G = R/4R = 1/4). Thus up-regulation is blown up and mapped between 1 and infinity, whereas down-regulation is compressed and mapped between 0 and 1. To eliminate this inconsistency in the mapping interval, one can perform transformations of the expression ratio, namely, logarithmic transformation. A better transformation procedure is to take the logarithm base 2 value of the expression ratio (i.e. log2 (expression ratio)). This has the major advantage that it treats
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