qBase

Relative quantification software for
management and automated analysis of real-time quantitative PCR data


This was the former website of the Ghent University software qBase for automated data-analysis of real-time PCR experiments, based on the formulas described in Hellemans et al., Genome Biology, 2007 (full text).
More than 4000 users worldwide have downloaded the software (2005-2008). As of February 2008, qBase has been phased out and the much improved successor qbasePLUS is now available from the real-time PCR data-analysis company Biogazelle.

Thank you for your interest, support and feedback the past 3 years!

Jan Hellemans and Jo Vandesompele
Ghent University, Belgium
February 25, 2008
Introduction

Gene expression analysis is becoming increasingly important in biological research and clinical decision making, with real-time quantitative PCR becoming the method of choice for expression profiling of selected genes. Advancements in chemistry and hardware have made the practical performance of real-time quantitative PCR measurements feasible for most laboratories. However, accurate and straightforward mathematical and statistical analysis of the raw data (cycle threshold values) as well as the management of large and growing data sets have become the major hurdles in this type of PCR based gene expression analysis. Since the software provided with the different detection systems usually does not provide an adequate solution for these issues, we developed qBase, a free software program for the management and automated analysis of real-time quantitative PCR data.

What is qBase?

qBase is a collection of macros for Microsoft Excel (currently only Windows version) for the management and automated analysis of real-time quantitative PCR data. The program uses a delta-Ct relative quantification model with PCR efficiency correction and multiple reference gene normalization. The qBase Browser allows data storage and annotation by hierarchically organizing real-time PCR runs into projects and experiments. It is compatible with the export files from many currently available PCR instrument softwares and provides easy access to all your data, both raw and processed. The qBase Analyzer contains an easy run (plate) editor, performs quality control and inter-plate calibration, converts Ct values into normalized and rescaled quantities with proper error propagation, and displays results both tabulated and in graphic format. The program can handle an unlimited number of samples, genes and replicates, and allows data from multiple runs to be processed together (preceded by an inter-run calibration if required). The possibility to use up to 5 reference genes allows reliable and robust normalization of gene expression levels. qBase allows easy exchange of data between users, and exports tabulated data for further statistical analyses using other dedicated software.

Download

qBase has been downloaded 4308 times in 109 countries.
The last qBase version is 1.3.5 and could be downloaded after free registration.
The qBase user manual and step by step tutorial were available as PDF files.

Citation

The qBase manuscript "qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data" is published in Genome Biology (Hellemans et al., 2007) and can be downloaded here.

Other qPCR related tools form our group

geNorm expression stability analysis of candidate reference genes for accurate normalization
[Vandesompele et al., Genome Biology, 2002]

RTPrimerDB: real-time PCR primer and probe database with currently 4000 real-time PCR assays
[Pattyn et al., Nucleic Acids Research, 2003]