i am integrating RNA-seq dataset which i mapped with kallisto against the reference genome. Now i have TPM for all of them which have been filtered for keeping only expressed genes.
My question is: in integrating the different datasets (belonging to different experiments) would you further normalize this whole dataset (e.g. log2 transform it and quantile normalize, or apply TMM, etc.. ), or would you go directly to the batch effect correction?
Thanks in advance