Prepare Your Data#
No matter whether you run the RAPDOR as a graphical user interface (GUI), a command line tool or within python, you need to make sure your data is in the expected format.
GUI and CLI#
For the CLI and the GUI you need to have two tabular files (e.g. tsv or csv files).
Intensity Table#
The first table contains an id, your Mass Spec Intensities of all fractions, conditions and replicates. It might also include additional columns with data. For instance it can look like the example below.
Note
It is highly recommended that the first column of the df contains no duplicates. It might not breakt the code but lead to unexpected behaviour
ID |
UniprotID |
Intensity RNase F1R1 |
Intensity RNase F2R1 |
… |
Intensity RNaseFree F1R2 |
|---|---|---|---|---|---|
VEGFA |
A0A0A0MR43 |
23.0689 |
22.814 |
… |
22.5512 |
… |
… |
… |
… |
… |
… |
Design Table#
The second tabular file has to be a design table. This will map the intensity columns from the Intensity Table to conditions.
Name |
Treatment |
Fraction |
Replicate |
|---|---|---|---|
Intensity RNase F1R1 |
RNase |
1 |
1 |
Intensity RNase F2R1 |
RNase |
2 |
1 |
… |
… |
… |
… |
Intensity RNaseFree F1R2 |
Control |
1 |
2 |
Note
The design table must have those column headers. Further only two level Treatments are supported by now.
Header |
Explanation |
|---|---|
Name |
The Names of the Columns that contain the Intensities in the Intensity Table |
Treatment |
A column containing names of the different treatments. |
Fraction |
The fraction to which those intensities belong to |
Replicate |
The Replicate to which those intensities belong to |
If your tabular files look like expected you can use them for the GUI or CLI.