Advantage and limitations of different measures of gene expression
in microarray data.

Expression index:
The magnitude of expression of a gene in one biological sample, based on weighted analysis of the probes for that gene. Expression indices indicate the amount of gene expression compared to the amount of other genes in the same sample. They can suggest the likely amount of error (the smaller the expression index, the greater the noise contribution). In themselves, expression indices indicate no comparison with other biological samples or conditions.

Expression difference:
The expression difference subtracts one expression index of a gene from one sample from an expression index of the same gene in another sample. It indicates the quantity of expression difference, but does not indicate the relative proportions of the two expression levels, which is more likely to have biological relevance.

Expression ratio:
The ratio between expression indices for a gene from two biological samples provides a good measure of possible up- or down-regulation of transcription between two conditions. It provides no perspective however on the overall sampling error and the overall level of transcription in the two samples.

Log2(ratio):
The log2 of the expression ratio represents the expression ratio in a manner such that positive and negative values appear equivalent; that is, a 1:2 ratio appears equivalent in magnitude to a 2:1 ratio. It still provides no correction for sample error and for overall transcription levels.

Centered log2(ratio)
The centered log2 of the expression ratio provides an expression ratio normalized to the overall levels of transcription of all genes in two conditions. This value is commonly presented as the most biologically relevant. However, it eliminates information about about overall transcription levels which might be relevant under conditions where a large number of genes are co-regulated; for example, down-regulation of of the entire protein synthesis apparatus (typically about 40% of a bacterial cell metabolism).