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- Sequencing depth: Say we are comparing gene counts in sample A against sample B. If you start out with 10 million reads in sample A vs 1 million reads in sample B, a 10 fold increase in expression in sample A is going to be purely due to its sequencing depth.
- Gene length: A gene that is twice as long is likely to have twice as many reads sampling it.
- Other factors like GC content
Most commonly done normalization
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