Robust ΔΔct estimate.

The ΔΔct method estimates fold change in gene expression data from RT-PCR assay. The ΔΔct estimate aggregates replicates using mean and standard deviation (sd) and is not robust to outliers which are in practice often removed before the non-outlying replicates are aggregated. The alternative of using robust statistics such as median and median absolute deviation (MAD) to aggregate the replicates is not done in practice perhaps because the distribution of a robust ΔΔct estimate based on median and MAD is not straightforward to deduce. We introduce a robust ΔΔct estimate and deduce an approximate distribution for it. Simulations show that when data has outliers, the robust ΔΔct estimate compared to the non-robust ΔΔct estimate leads to significantly reduced confidence interval length and a coverage close to the nominal coverage. The analysis of an RT-PCR data from a Novartis clinical trial demonstrates benefit of a robust ΔΔct estimate.