Chapter 12 Data Analysis

There are many types of analysis you can perform with Tercen. To see the some example cases, please explore the collections.

Go to https://tercen.com/explore/tab/collections.

Each project in this page, is an example project and in each project is a workflow containing the data analyis steps. The steps usually contain a computation called an operator. For a complete list of operators see the operator catalog.

Typical steps taken during an ‘omics’ analysis are the following:

  • create or join a team for the analysis
  • create the new project inside the team
  • upload the data to the new project
  • create a workflow to perform the following
    • overview of raw data
    • quality check (outlier samples, batch effects)
    • normalization (if there is a systematic effect)
    • transformation (usually a log function)
    • exploration
      • heatmaps. PCA, tSNE, fold changes, profiles
      • clustering
    • statistical testing
      • t-test, anova
    • biological interpretation
      • pathway analysis, enrichment analysis
      • network analysis

The parameters you adjust for are:

  • kicking out samples (outliers)
  • normalization or not (depends on the data)
  • statistical test (t-test or anova)

Overview of raw data

Use a the following visuals to get an overview.

  • Heatmap visuals
  • Profile visuals

Quality check (outlier samples, batch effects)

There are a range of quality checks Here are some examples:

  • Heatmap visuals
  • Box plots visuals

Normalization (if there is a systematic effect)

There are a range of normalization techniques Here are some examples:

  • vsn_operator
  • normalizer_operator

Transformation (usually a log function)

There are a range of transformation techniques Here are some examples:

  • log_operator
  • asinh_operator

Exploration

There are a range of exploration techniques Here are some examples:

  • heatmap visuals
  • dimension reduction (PCA, tSNE, UMAP)
  • fold changes
  • profiles
  • clustering

Statistical testing

There are a range of statistical techniques Here are some examples:

  • ttest_operator
  • anova_operator

Biological interpretation

There are a range of statistical techniques Here are some examples:

  • fsgea_operator
  • pathway analysis
  • network analysis