What mathematical model does the Illumina Eco analysis software use for relative quantification experiments?
The Illumina Eco analysis software uses the ΔΔCq method (Livak et al., 2001), which is the most commonly used analysis method for relative quantification. The ΔΔCq method reports fold change in gene expression of a target gene relative to that of a reference gene and reference (calibrator) sample. The reference gene is typically a housekeeping gene such as GAPDH, β-actin, β2-microglobin or HPRT. The choice of reference sample can vary depending on the type of gene expression experiment. For example, a reference sample might be an untreated control sample relative to a treated sample, normal tissue relative to diseased tissue, or liver relative to brain. For the ΔΔCq method to be valid certain assumptions must be met. First, the reference gene must be stably expressed between different cells of tissues and unaffected by any experimental treatment. Second, the amplification efficiencies of both target gene and reference gene must be approximately equal. Both of the conditions should be e
