RDML format recommended for quantitative PCR data

CONDUCTING a PCR (polymerase chain reaction) experiment is a routine operation these days, but like many aspects of modern laboratory science the bottleneck comes in the analysis of the large quantities of data generated.

Now a researcher at the Academic Medical Centre in Amsterdam, Netherlands, Jan Ruijter, says that the RDML (Real-time PCR Data Mark-up Language) is the recommended option and is becoming the industry standard for qPCR data exchange and storage.

RDML is an open-source format that was created to encourage the exchange, publication, and re-analysis of raw qPCR data. Files are written in a database structure based around an experiment, rather than a PCR run.

In 2009, the MIQE guidelines (Minimum Information for Publication of Quantitative Real-Time PCR Experiments) were introduced to standardise the presentation of these data. According to Ruijter, QbasePlus software from Biogazelle is the only third party qPCR data-analysis software that is MIQE compliant.

LinRegPCR is an independent program for primary analysis of raw qPCR data. It calculates Cq and PCR efficiency values based on fluorescent amplification curves. Ruijter and colleagues first launched LinRegPCR in 2003, for the analysis of quantitative PCR data from individual amplification curves (single curve efficiency estimation). As of today, LinRegPCR can export raw data, baseline, efficiency values, Fq and Cq values to RDML. Such an RDML file can then be imported in QbasePlus, combining raw qPCR data processing (from LinRegPCR) with relative quantification and statistical analysis (in QbasePlus) in a continuous workflow.

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