Loading Data

First a few quick words about the data set. We’ll be working with data coming from 3 runs (plates in the qPCR instrument): Run1Run2 and Run3

The data consist of Cq values for:

  • 3 reference target genes: Stable, Nonregulated, and Flexible
  • 3 target genes of interest: Duvel, Leffe, and Palm

Each is measured twice (= technical replicates) in 16 different samples. Half of the samples have undergone a treatment, half of them are untreated control samples.

The data set also contains a series of standard samples consisting of a four-fold dilution series of cDNA for each target gene. These measurements allow to generate a standard curve from which target-specific amplification efficiencies can be calculated. Finally, negative controls (No Template Controls) have been measured. The goal of the analysis is to identify target genes of interest that have different expression levels in the treated samples compared to the untreated control samples.

In GeneExpression load CFX run files Run1Run2 and Run3:

  • Click the Import runs button to open the Import Run window
  • Click the Browse button to go to the directory that stores the files containing the qPCR data

Select the 3 run files simultaneously by holding the Ctrl key on your keyboard during the selection in Windows or the command button in MacOSX.

  • Click the Open button

Now you go back to the Import Run window, click the Next button (purple)

  • qbase+ tries to recognize the format of the selected import files. If only one format matches the files (as in our case CFX), it is selected and the quick import option is enabled. Click the Finish button.

In the Imported run names area on the Import run page you should now see the names of the 3 run files. If these are the correct files, click the Next button at the bottom of the page.