Loading the Data with the GUI
The basis of half-life calculation is data from microarray or RNA-seq experiments. Before accessing and
using the methods provided by HALO you thus have to load your data from a single file and specify the
details about the data organization. For a detailed description of the input format please see the section
File formats. Below you can find an overview over the steps of the data loading
process with the GUI.
The data loading menu
The menu for data loading is always visible from the start in the main panel of the GUI.
You can choose your data file here with the Browse button.
Choosing your input file
Your data file will be processed before loading, so that
you can choose the column labels that define newly transcribed, pre-existing and total RNA, as well as the label for the column
containing the probeset ids. Please note that if you choose an unequal number of RNA for the three cases, you
will be limited in the subsequent analyzes. You can also define whether your data is in log or linear scale.
If your data file also contains additional attributes, you are asked if you want to load these with your data.
Attributes can be saved with the data for further uses, and several methods of the HALO software package require
attributes like gene names or present/absent calls. You can load these directly with your data or over the
Add attributes/sequences button afterwards.
Please note: You should never load present/absent calls together with other attributes! Since present/
absent calls are attributes with only very few values, they are saved differently from other attributes in
order to speed up the loading process. If you load other attributes in the same way, further procedures
might not work! You will be asked if your attributes are present calls whenever you load attributes.
Loading additional attributes
The Add attributes/sequences button offers you the possibility
to load files containing one or more attributes (for information on file format see
File formats), one menu point for the loading of a multiple fasta file and also provides you with
the possibilty to load attributes from your original data file. The multiple fasta file should
contain sequences for every of your probesets (probesets with no matching sequence will be ignored otherwise)
and a gene name in the header that is identical to the name of the corresponding attribute. You can thus
use a multiple fasta file only in combination with an attribute defining gene names for your probesets.
You can choose the column that contains the gene name at the example of the first sequence from your file.
After you have loaded the data you are able to access two new menus: The Filtering
and the Normalization menu. You can extend the GUI to show these menus by
clicking on the corresponding menus in the menu bar: Filter Data and Normalization → Normalization.
If you have loaded gene names and sequences you can now also evaluate your data with the
Quality control menu in the menu bar.