The settings menu
The settings menu allows you to enter a number of constant values, so that you do not have to input these at
every relevant point. You can always change these values.
Set alpha function
In the current version (1.3) you can choose between two different alpha functions that are used for half-life
calculation. The first of these is the default method, which always returns 1. The second method models the cell
division; for this method you have to enter the numerical parameter ccl (cell cycle length).
Set labeling time
Here you can enter a constant labeling time that will be used for all subsequent analyses, e.g. half-life
calculations.
Set path to R
For quality control you have to have R
installed. You can enter the path to it's bin folder here.
Set maximum/minimum half-life
For ratios equal to or larger than 1 the half-life calculation is difficult, resulting in negative or NaN values. This problem is avoided by defining a maximum and minimum half-life. Default values for this are 10000 for maximum half-life and 5 for minimum half-life. You can customize these values with this menu point.
Set replicate
If you want to keep using only one replicate for all your analyzes, you can enter its number (starting from 1) here
and won't have to enter it every time.
Set gene name attribute label
Per default the label of the gene name attribute is set to gene_name, which may differ from the label
in your data. When you load a multiple fasta file or try to filter according to PQS values, for which gene names
are needed, you will be asked to change the label to one that fits your data. You can also use this menu point to
change it previously.