Getting started

This Wiki page is a part of piLINCS quick help. This page describes how to interactively browse LINCS proteomic profiles available through piLINCS.

Assuming that everything works fine, piLINCS should start with its HOME tab open. Other tabs that allow to navigate between different views are listed in the bar at the top of the page. In order to explore these different options while browsing data interactively, one can jump between views/tabs:

• piLINCS HOME
• Raw data tab
• Profiles tab
• Merged profiles tab

The three basic 'views' listed above enable access to three types/levels of profiles that can be accessed and exported through piLINCS:

• Raw data: high level data from Panorama with individual measurements using the QC+NORM normalization
• Profiles: data reorganized as actual profiles with individual replicates
• Merged profiles: data reorganized as merged/collapsed profiles with replicates collapsed into averaged profiles

The following visualization methods are used for these different views:

• Raw data: this tab uses a tabular format to display individual data points (peaks corresponding to a specific analyte/peptide), with links to Panorama
• Profiles: this view uses a bar chart to represent the entire (P100 or GCP) profile for each technical replicate; the height of bars is used to represent the normalized peak area value (relative abundance of an analyte/peptide) displayed as a real value in the 'Raw data' tab
• Merged profiles: this view uses a bar chart to display concatenated P100 (blue) and GCP (red) profiles, as long as data is available for a given (cell type, perturbation, dose, time) tuple

For illustration of these different view, see a poster poster with examples and screen shots.

These three different levels/types of profiles are also used to export data under the Export tab.