quantile normalization for normalized values

Question

[BenHu]

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,

Answer 1

[Ram]

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.

[igor]

Some previous discussions that might be helpful:

• Differences between FPKM and FPKM-UQ files in gene expression analysis
• TCGA/GDC FPKM vs FPKM-UQ