Biclustering Analysis

This operation performs a Biclustering Analysis on Aligned Peak Lists.

Usage

You can execute this operation by clicking the button or following the menu Analysis/Biclustering Analysis.

A dialog will appear allowing you to select the following options:

• Data: Labeled Aligned Peak List Set or Unlabeled Peak List.
• Minimum inter-sample presence: masses must be present at least in this percentage of the total samples.
• Maximum inter-sample presence: masses must be present at maximum in this percentage of the total samples.
• Use Missing Values.
• Bicluster type: pattern type of target biclusters. It can be a Presence pattern, an Absence pattern or a Presence-Absence pattern.
• Biclustering algorithm: biclustering algorithm to use. It can be BiMax or Bibit.
• Biclustering mode: specify whether samples or masses are passed in rows to the biclustering.
• Min. samples in bicluster: minimum number of samples in a bicluster.
• Min. masses in bicluster: minimum number of masses in a bicluster.
• Class biclusters: Check if you want to retrieve only class-biclusters.
• Output directory: directory to store the biclustering results.

Output and visualization

As a result of this operation, a new Biclustering is added to the clipboard. Every time a new Biclustering Result is accessible, it can be inspected with the Bicluster Explorer View.

Export results

You can export the biclustering results using the "Export" menu.

This menu offers you the following options:

• Export table to CSV: allows you to export the biclusters table as a CSV file. This can also be done by clicking the right-corner button of the table () and choosing the "Export to CSV" option. You can find more information about this at section Export results.
• Export heat map to image: allows you to export the biclusters heatmap as an image. A dialog will appear allowing you to select the file to save the image..
• Export selected bicluster: if you have selected a bicluster in the table, this option allows you to export its information into a file.

You can also export the selected bicluster information by doing right-click in the bicluster information area (at the bottom of the Bicluster Explorer View), a context menu will appear allowing you to:

• Copy to clipboard: copy the selected bicluster information into the clipboard.
• Export to file: export the selected bicluster information into a file.