RNA-seq & Transcriptomics Analysis
Transcriptomics
Plan expression analysis and comparisons around biological replication, sample metadata and the study design.
Questions to discuss
- How does expression differ between the specified study groups?
- Do exploratory patterns suggest batch effects or sample inconsistencies?
- Which functional themes are supported by the expression results?
Input for review
- Reads or a count matrix with gene identifiers and processing history.
- A sample sheet linking every matrix column or file to its biological sample.
- Condition, batch, biological unit, pairing and relevant covariates; organism and reference information.
Analysis planning
- Review study design, count provenance and the proposed contrasts.
- Inspect quality, sample relationships and potential confounding.
- Agree on an expression model, contrasts and multiple-testing approach.
- Summarize results and functional analyses with their assumptions.
Reporting options
- Exploratory quality plots and sample summaries.
- Differential-expression tables for agreed comparisons.
- Functional summaries, figures and method documentation as scoped.
Interpretation
Batch and condition must be distinguishable for the intended comparison. Cells, reads or repeated measurements do not automatically provide independent biological replication.