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count-matrix-qc

separate

Quality control and exploration of RNA-seq count matrices before differential expression. Use when checking library sizes and composition, choosing VST vs rlog for visualization, running PCA and sample correlation, detecting outliers with Cook's distance, deciding how to handle known vs unknown batch effects, screening for sample swaps, or judging whether a sample or design is too compromised to test.

When to use

• checking library sizes and composition
• choosing VST vs rlog for visualization
• running PCA and sample correlation
• detecting outliers with Cook's distance
• deciding how to handle known vs unknown batch effects
• screening for sample swaps
• judging whether a sample or design is too compromised to test

When not to use

• differential expression testing
• feeding transformed matrices into the count model

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