Statistical analysis of real-time PCR data

BMC Bioinformatics. 2006 Feb 22:7:85. doi: 10.1186/1471-2105-7-85.


Background: Even though real-time PCR has been broadly applied in biomedical sciences, data processing procedures for the analysis of quantitative real-time PCR are still lacking; specifically in the realm of appropriate statistical treatment. Confidence interval and statistical significance considerations are not explicit in many of the current data analysis approaches. Based on the standard curve method and other useful data analysis methods, we present and compare four statistical approaches and models for the analysis of real-time PCR data.

Results: In the first approach, a multiple regression analysis model was developed to derive DeltaDeltaCt from estimation of interaction of gene and treatment effects. In the second approach, an ANCOVA (analysis of covariance) model was proposed, and the DeltaDeltaCt can be derived from analysis of effects of variables. The other two models involve calculation DeltaCt followed by a two group t-test and non-parametric analogous Wilcoxon test. SAS programs were developed for all four models and data output for analysis of a sample set are presented. In addition, a data quality control model was developed and implemented using SAS.

Conclusion: Practical statistical solutions with SAS programs were developed for real-time PCR data and a sample dataset was analyzed with the SAS programs. The analysis using the various models and programs yielded similar results. Data quality control and analysis procedures presented here provide statistical elements for the estimation of the relative expression of genes using real-time PCR.

MeSH terms

  • Analysis of Variance
  • Animals
  • Base Pair Mismatch
  • Cloning, Molecular
  • Computational Biology / methods*
  • DNA Probes
  • DNA, Complementary
  • Data Interpretation, Statistical*
  • Gene Expression Profiling
  • Humans
  • Mice
  • Models, Biological
  • Models, Statistical
  • Oligonucleotide Array Sequence Analysis
  • Polymerase Chain Reaction
  • Programming Languages
  • Quality Control
  • RNA / chemistry
  • Regression Analysis
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • Sensitivity and Specificity
  • Software
  • Statistics as Topic


  • DNA Probes
  • DNA, Complementary
  • RNA