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What is a good RNA seq normalization method that allows for across sample comparisons, and allows between transcripts comparisons as well? I read that TMM for example allows across sample comparisons but not between transcripts. On the other hand, I read that TPM is not good enough for between sample comparisons

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Unfortunately, there doesn't seem to be any such metric. We use counts two-way normalized across genes and samples but even that is approximate as there is no way to ensure that all genes being counted are definitely expressed across all samples, and that all samples are sequenced to the exact same depth and that there are no batch effects and that biological differences are reflected with full fidelity.

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