stephaniehicks/qsmooth

Questions on the advantages of qsmooth

Closed this issue · 2 comments

chilampoon commented

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:

  1. preservation of global differences in distributions corresponding to different biological conditions
  2. 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.

stephaniehicks commented

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

stephaniehicks commented

Closing this issue.