nondetects

'nondetects' is an R package to address the analytical challenges posed by non-detects in quantitative real-time PCR (qPCR) data, a common issue where specific reactions fail to generate a detectable signal. This tool highlights the often overlooked problem of qPCR non-detects, demonstrating through analysis that conventional methods of handling such data lead to biased results. Furthermore, nondetects challenge the assumption that these non-detects represent data missing completely at random, suggesting instead that they likely signify data missing, not at random.

To improve the accuracy of gene expression analysis and avoid bias, a model for the missing data mechanism can be introduced to handle nondetects. This approach allows non-detects to be directly modeled as missing data, significantly reducing absolute and differential gene expression estimation bias. As a result, it enhances the reliability of qPCR data analysis.