Normalization with Interplate Calibrators!!!
To normalize Cq values measured in different runs, select Normalization with Interplate Calibrators in the Pre-processing menu in the Data Editor, to open a dialog box. Make sure that the data sheet contains one classification column that indicates whether a sample is an interplate calibrator (#IPC) or not, and one that indicates which plate the samples belongs to (#Plate). The IPC data is given in one row for each plate. If there are more target genes (columns) than measurements in the IPC samples, just leave the extra cells empty. GenEx will either use the column average of the IPC samples to fill the cell, or if all IPC samples have empty cells in that column, use the row average to fill the cell. If each of the target genes where measured in the IPC samples, make sure that they are given in the corresponding columns.
Select the classification column that indicates whether the row (sample) is an IPC or not, and choose which of the values in this column that represents an IPC-sample. Then, select which classification column that indicates which plate the sample was analyzed on. If several different genes were measured in the IPC sample, the average of these can be used to normalize each sample with. If the check box IPC mean value is not used, each column will be normalized against the IPC data in the same column (empty cells in IPC samples are filled as stated above). Press Apply to normalize data and remove the IPC data from the sheet.
GenEx mean centers the IPCs before normalization using the following equation, where m is the number of interplate calibrators in run "m", and n is the total number of interplate calibrators.
