Dear all, I would like to ask your opinion on the possibility of combining DRIMseq with RUVseq to adjust a statistical model for the presence of possible sources of unwanted variability, aka latent variables. I have already been able to use RUVseq very effectively for DGE analysis and would like to better understand if this possibility also exists for DTUs.
Do you have any experience and can you give any suggestions on how to integrate the two packages? Is it possible to estimate unwanted variation factors, e.g. with the RUVg or RUVr function from the transcript count matrix, and then add the obtained covariates along with the variable of interest to the model for DTU by DRIMseq? Thanks in advance. Luca