normalization

[laetitiacollet]

Hi,

I would like to apply scissor on my bulk RNA seq data but I do not know how to normalize bulk RNAseq data for scissor. In your paper your talk about quantile normalization but my data set is small ( around 100 samples) and I am affraid that quantile normalization will decrease the true differences between samples / class.

Witch normalization would you advise ? What do you think about VST or log(TPM + 1) normalization.

thanks in advance for your reply