Study Preferences Guide

This guide helps new users understand and configure Study Preferences in Omics Studio. Study preferences establish default values that apply across analyses, giving you a consistent focus and saving time later. The settings are organized into four sections: Identifier Preferences, Expression Preferences, Statistical Preferences, and Database Preferences. All selections can be modified when performing specific analyses, but setting sensible defaults here streamlines your workflow.

Overview

When you open a study in the Explorer, click Study Preferences in the left-hand menu. A panel opens with guidance text explaining that preferences maintain a specific focus right from the start and can be adjusted during analysis creation.

Scroll down the panel to see all available options. At the bottom, you’ll find Reset Study Preferences and Save Study Preferences buttons to discard or save your changes.

1. Identifier Preferences

Identifier preferences determine how expression and metabolite values are mapped in downstream analyses.

• Select the Expression Identifier – Choose the identifier for your expression dataset. Options include Uniprot ID, Ensembl ID, Gene Name, and Protein Name. Gene Name is the default, but selecting Uniprot ID or Ensembl ID can improve mapping in proteomics or transcriptomics studies respectively.
• Select the Metabolite Identifier – Set how metabolites are represented. Choices are ChEBI ID, InChI, and Metabolite Name (default). Standardized identifiers like ChEBI ID help ensure accurate pathway mapping.

Tip: You can clear the current selection using the small “×” beside the field and choose another identifier from the dropdown.

2. Expression Preferences

These settings filter your expression data before analysis.

• Valid Value Threshold – Define the minimum percentage of non-missing values required for a feature (e.g., 70%). Omics Studio discards features with less valid data, improving reliability.
• Pre-select Samples – Optionally restrict analyses to specific samples. Clicking the field opens a list of available samples (e.g., Sample1, Sample2); select one or multiple samples to focus on a subset. Remove selections using the small “×” next to each tag.

3. Statistical Preferences

These defaults apply to differential analyses and subsequent enrichment tests.

• Comparisons – Choose which statistical contrasts to use. Available comparisons correspond to group contrasts defined during statistics generation. Examples: GroupA vs GroupC, GroupA vs GroupB, GroupB vs GroupC.
• P-value – Set a significance threshold (e.g., ≤ 0.05). Features with p-values above this cutoff will be excluded by default.
• Adjusted P-value – Similarly define an FDR-corrected significance threshold (e.g., ≤ 0.05). Using both p-value and adjusted p-value thresholds reduces false positives.
• Log2 Fold Change (up-regulated) – Minimum fold-change for up-regulation (e.g., ≥ 1), representing genes/proteins with at least a twofold increase.
• Log2 Fold Change (down-regulated) – Maximum fold-change for down-regulation (e.g., ≤ –1), capturing at least a twofold decrease.

These thresholds serve as starting points; they can be adjusted in each enrichment analysis as needed.

4. Database Preferences

Set default annotation databases for enrichment analyses. Clicking this field reveals available knowledgebases; selections depend on your data type (proteomics, metabolomics, transcriptomics). Examples include:

• Homo sapiens | Pathways | Reactome (Source ID ChEBI | Metabolomics)
• Homo sapiens | Pathways | Reactome (Source ID Ensembl | Transcriptomics)
• Homo sapiens | Pathways | Reactome (Source ID Uniprot | Proteomics)
• Homo sapiens | Cellular Components | Reactome (Source ID ChEBI | Metabolomics)
• Homo sapiens | Biological Process | Gene Ontology

Selecting a database here will prepopulate the database choice in ORA or GSEA wizards, but you can always choose different databases later.

Saving or Resetting Preferences

Once you have set your defaults, click Save Study Preferences to apply them. The settings persist for your current study and will be suggested in all future analyses.

If you want to revert to the original defaults, click Reset Study Preferences before saving. Both buttons are located at the bottom of the panel.

By configuring these study preferences, you streamline later analyses and ensure that identifiers, thresholds, and databases align with your experimental design. You can adjust any of these settings during specific analyses, but establishing thoughtful defaults will help maintain consistency and improve reproducibility.