Definitions and concepts

Target
The generic term used for the DNA sequence to be quantified. It typically refers to a gene, but could also refer to a specific transcript or a genomic locus. Two target types are recognized: targets of interest and reference targets.

Cq value
The MIQE standard name for Ct (cycle threshold), Cp (crossing point), or other instrument specific quantification value name.

Run
Collections of qPCR data coming from a single plate, array, rotor or chip (depending on the instrument being used).

Experiment
The set of data (stored in one or multiple runs), annotations and settings used for qPCR data analysis.

Project
Logical groups of related experiments.


Inter-run calibration
A calculation procedure to detect and remove inter-run variation.

Sample
In qbase+, a sample is defined as the nucleic acid dilution on which the qPCR measurement is performed. According to this definition, a serial dilution made from a single RT reaction or DNA sample would consist of different sample names.


RDML
A universal, open and XML based data format for the exchange of qPCR data, recommended by the MIQE guidelines.

Reference target
The targets that will be used to normalize the qPCR data. In the context of gene expression analysis, this target type used to be referred to as housekeeping gene.

geNorm
The algorithm developed by Biogazelle co-founder prof. Jo Vandesompele (Genome Biology, 2002) to determine the expression stability of selected (candidate) reference targets. It can be used in geNorm pilot studies to identify the optimal set of reference genes to be used in follow up studies, or later on to verify the expression stability of selected reference targets.

Sample property
Two types of sample properties are used in qbase+. There is a set of predefined sample properties such as sample name, sample type and quantity. Custom sample properties can be added to link (usually annotation) information to samples. For each sample, a sample property value can be entered. For example, the sample property ‘gender’ may have sample property values ‘male’ and ‘female’.

Normalization
The procedure by which technical sample specific variation (e.g. differences in total amount of cDNA) is corrected for. Normalization is typically performed by means of reference genes, but alternative approaches are available.

Result scaling
The results of a relative quantification analysis do not have a particular scale. Because of this they can be multiplied (or divided) by a common factor. This process will alter the actual values, but not the sample to sample relationships (i.e. the fold changes). It does not alter the results but may facilitate interpretation, for example by making all results relative to a control sample.

Workspace
The workspace is the central location in which qbase+ stores all its information: data, annotation and settings.