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quantile normalization for normalized values

Hi, quantile normalization is able to correct the imbalance in the read counts across multiple samples. my question is that whether quantile normalization can adjust the imbalance in the normalized reads, such as TPM or FPKM across different samples. Thanks in advance! Best,

rna-seq

1 answer

TCGA uses FPKM-UQ, so while I am not sure how valid this sort of double-normalization is, TCGA seems to have a rationale for doing it. I'd recommend you search for some sort of publication explaining FPKM-UQ.

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