( )? P This application ...)Extended data analysis using DeCyder EDA

This application note describes the use of DeCyder Extended Data Analysis Software (DeCyder EDA) to answer these remaining questions, using an example from a human cancer study.

Workflow
The analysis workflow for DeCyder EDA is shown in Figure 1.

Set concept
DeCyder EDA uses a set of data for analysis. A set is a group of spot maps with matched spots—a group of spot maps and proteins. A set of data can be displayed in several ways depending on the context, for example as a heat map where each row represents a protein and each column represents a spot map.

Setup
The original data set consists of the Biological Variance Analysis (BVA) workspaces imported and linked in the DeCyder EDA workspace. Before any analyses can be performed, an EDA workspace and a base set must be created from the BVA workspaces. Setup consists of three main steps:
1. Workspace: creating an EDA workspace by importing and linking BVA workspaces.
2. Experimental design: assigning experimental groups and conditions for the different samples included in the EDA workspace.
3. Base set creation: creating the base set automatically or manually by filtering and normalization of the data.

Calculations
After setup is finished and a base set is created, calculations are enabled. The different calculation methods are divided into four main groups:
• Differential expression analysis
• Principal components analysis (1–3)
• Pattern analysis (4–11)
• Discriminant analysis (12–16)

There are a number of subanalyses within each of the calculation groups. The different calculatio
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