I have two matrices with RNAseq UMI counts, sequenced in 2 different moments (from same person, same lab, but different timing).
- Matrix-1 contains samples of: Primary breast cancer, Metastasis (several different tissue), normal breast tissue.
- Matrix-2 contains samples of normal tissue of the site of one of the metastasis (normal tissue of just one of the metastasis).
What i will have to work on are only the primary and metastasis samples. However, in the future i might need to do some analysis using the normal samples too.
So first, I have to perform normalization, which i am going to do with vst() function from the R package DESeq2. My question is: should i normalize separately Matrix-1 and Matrix-2? Or merge the 2 matrices and normalize all together? Or drop the normal breast samples from matrix-1 and normalize the matrix with only the primary and metastasis samples?
I have to work mostly on primary and metastasis, but to avoid to go back again to raw counts and normalize again the data, I wanted to normalize and keep in a folder the normal samples too.
Thanks for any help/suggestion!