FAQ

Which omics types are supported?

Proteomics, phosphoproteomics, and RNA-seq.

Why does my table not appear after selecting species?

Most common reasons:

• table name does not follow expected species prefix
• table_metadata entry is missing
• table naming pattern is inconsistent with the selected species

Which identifier columns are required?

For data tables:

• Gene_Name
• Gene_ID
• Protein_ID

For phosphoproteomics, add:

• pepG

Why is annotation required?

Annotation is used for gene-level context and transformations. BRIDGE expects an annotation table that matches species and genome version.

What is the expected datapoint naming format?

Datapoint columns should end with replicate index using underscore, for example:

X6.hpf_1

Why do no genes appear after filtering?

Likely causes:

• thresholds too strict
• selected contrast has weak signal
• poor ID overlap across integrated datasets

Try more permissive thresholds first, then tighten.

What is the difference between raw and processed integration?

• Raw integration compares loaded values directly across selected columns.
• Processed integration filters by significance first, then intersects IDs.

Can I load multiple datasets in one session?

Yes. This is required for integration workflows.

Can I use preprocessed objects?

Yes. During database generation you can add precomputed processed objects (for example SummarizedExperiment) so BRIDGE can reuse them.