Normalization with the GUI
If you want to calculate half-life values for your data, you first have to determine correction
factors for the normalization. For this purpose the HALO GUI provides the Normalization menu, where
you can choose between a set of methods for the normalization of your data.
Extending the menu
Normalization is available after you have loaded the data.
You can access the menu by through clicking the menu option
labeled Normalization from the Normalization menu in the menu bar.
Normalization methods
In the current version (1.3) you can choose between two normalization methods; if you have loaded
data in unequal numbers only the second of these is accessible.
- Linear Regression
This method performs normalization through a simple linear regression. You can choose between
calculating the ratio over the average of all replicates (default), the average over the ratios for each
replicate or one replicate alone for this procedure.
- Median half-life based
This method is based on a median half-life that you have to calculate separately and can enter
in the popup dialog. You will have to choose at least one half-life calculation method, labeling time and
(optionally) a replicate for the ratio calculation in this method.
In order to start the process you have to click the Start button.
Your resulting correction factors will then be displayed and used automatically for the half-life calculation.
Plotting the results
If you have chosen linear regression as normalization method, you have the possibility to plot the results.
In the graph your data will be shown as scatter plot (blue), and the linear regression line will be displayed in
red. This procedure might take a couple of seconds. You can save this graph or the values as a plotting file.
You can always save plots and change properties through right clicking in the figure.
Subsequent steps
Normalization unlocks the Half-Life menu in the menu bar.