This 2.5-minute video shows how to identify DEGs using the Compare 2 Groups tool included in the Basic Plug-in for Subio Platform, and how suspected batch-effect samples can influence the results.
Differential expression analysis can be strongly affected by batch effects. When batch effects are suspected, it is not enough to simply run the analysis. You may need to consider normalization or batch correction methods, and carefully decide whether suspicious samples should be included or excluded.
In this video, we perform DEG extraction under two conditions: with the suspected samples included, and with them excluded. We then visualize the results using heat maps and show that the DEG patterns can change dramatically depending on this decision.
Want to learn more about RNA-Seq DEG analysis?
→ RNA-Seq Tutorial - Identifying Differentially Expressed Genes (DEGs)
Previous video in this series:
→ Short Instruction 2: Refine Your Dataset with Filtering
Detailed explanation of the data used in this video
→ Apparent Differences Created by CPM Normalization and Potential Biases at Multiple Steps