Half-life calculation with the GUI
After loading and normalizing the data you can calculate the half-lives.
Extending the menu
You have to load the data and perform normalization before you can access the half-life
calculation menu. After doing so you can extend the panel through simply clicking on the
menu labeled Half-Life calculation in the Half-Life
menu of the menu bar or by pressing Ctrl+H.
Adding Half-life calculations
In the current version (1.3) three methods for half-life calculations are implemented. You
can include as many different methods as you want through subsequent clicking on the
Add calculation button. A popup dialog will
appear where you can choose between the three methods:
You can also define two additional parameters:
- Newly transcribed/Total based
This method uses the ratio of newly transcribed to total RNA and the correction factor c_l for half-life
- Pre-existing/Total based
For this method the ratio of pre-existing RNA to total is used, as well as the correction
- Newly transcribed/Pre-existing based
The last method uses the ratio of newly transcribed to pre-existing RNA and the correction factor c_lu.
Please note that you can not change the half-life methods defined for normalization if you chose
median-based normalization, because this method only provides one correction factor instead of all three.
- Labeling time
In the field Enter time you can enter a custom labeling time
for each calculation. You can also enter a constant labeling time in the
Settings menu that will then be used for every calculation.
Instead of using an average over all replicates (as defined in normalization) you can also use a specific
replicate. This is optional; if you prefer the average over all replicates you can just leave the field
empty. Again you can enter a constant replicate in the Settings menu.
An overview over all your chosen parameters and methods can be accessed via the
Display choices button. In order to start the calculation you have to click the Start button.
Plotting the results
After calculating the half-lives you can plot the results. On the x-axis the half-lives are listed, while the
y-axis displays the relative frequency of each half-life. For each method that you used, a different
graph will be generated. You can save a plotting file that contains all values for all methods.
Saving the half-life values
You can save the calculated half-life values via the Save button. You
can choose if you want to save only values from one calculation, in combination with one or more attributes,
or save all calculations without attributes. For this last method you can choose between three types of values;
the half-life values, the ratio values used for these or both. For details on the output format see the
File formats page.