I want to generate TMM- Normalized fpkm values RNASeq data 5 time point data for male and female. I am very much confused how to generate these values.
1) Is it applying TMM to fpkm or apply TMM to raw counts and log transform the values to fpkm ?
2) Is it acceptable to use TMM- Normalized fpkm or should people use TMM- normalized raw count directly ?
3) TMM- normalized fpkm does it mean it normalized twice and is it necessary.
Can anyone provide the step wise commands in R to generate TMM- normalized fpkm matrix
Thanks in advance