Dear All,

I have been trying to learn about RNA-seq differential analysis and have encountered some questions regarding normalization and standardization. My questions primarily focus on the following points:

**Is standardization (also known as Z-Score Normalization) a subset of normalization?**Are the two concepts related in such a way that normalization encompasses standardization?**In differential expression analysis, or more broadly in bioinformatics, do normalization and standardization have essential differences?****In the DESeq2 literature, the term "normalization" is frequently used**. However, after closely examining its steps and principles, I feel that it aligns more with the meaning of standardization. Is it because DESeq2 does not use Z-Score standardization, hence the use of the term "normalization" for the sake of accuracy in the article's narrative?My current understanding is that standardization (not limited to Z-Score here) aims to eliminate systematic errors/bias, while conventional normalization techniques, such as logarithmic transformation or min-max normalization, primarily serve to scale the data. Is this understanding correct?

I am still struggling to distinguish when to use normalization versus standardization in daily bioinformatics analysis.

**How can I determine which method to apply in different scenarios?****Can normalization and standardization be used simultaneously? If so, is there a specific order for applying them? Are there theoretical foundations guiding whether to use one before the other?**

During my studies, I have consulted many resources, but the more I read, the more confused I become. Therefore, I am seeking some assistance.

I appreciate any insights or clarifications you can provide!

Thank you!