Questions on the advantages of qsmooth
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Hello,
I have been confused about the differences between doing qsmooth for the whole dataset and doing quantile normalization in each tissue (tissue-aware QN) since I read the YARN and qsmooth paper. The qsmooth paper stated that the advantages of qsmooth include:
- preservation of global differences in distributions corresponding to different biological conditions
- non-reliance on external information
I think these are related to the weights assigned to each quantile, so the tissue-aware QN cannot keep global differences? Then how to explain this difference? And is qsmooth really better than tissue-aware QN? Thanks.
Hi @chilampoon,
Thanks for your interest! Yes, you are correct. The weights assigned to each quantile in qsmooth are related to the amount of variability within and between biological groups.
Regarding tissue-aware QN -- I am not an author on the YARN paper (https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1847-x) and would suggest reaching out to the first author to find out more details.
Hope this helps!
All the best,
Stephanie
Closing this issue.