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gene-protein-expression-matrix-normalization

separate

Use when normalizing bulk gene or protein expression matrices with log2 transform, z-score standardization, or min-max scaling before downstream visualization or exploratory analysis. NOT for count-model normalization such as TPM/DESeq2 size factors, batch correction, or single-cell preprocessing.

When to use

• "Normalize this gene expression matrix with log2"
• "Do z-score scaling across samples"
• "Map protein abundance values into 0 to 1"

When not to use

• Count-model normalization such as CPM, TPM, TMM, or DESeq2 size factors
• Batch correction or covariate adjustment
• Single-cell preprocessing workflows
• Matrices that contain missing, `Inf`, or `NaN` values unless they are cleaned first

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