Hi Biostars community,
Let me explain my situation: I have to determine the expression of different genes in different tissues. Each tissue has a biological replicate coming from another individual (the only difference is 3 months in term of age). These two individual are healthy so my expectation is that there is no a significant difference in gene expression between them. So it is not useful in this case to perform DEA with DESeq and so on.
I calculated TPM values from raw reads with Salmon. I know that there are a lot of posts about this but in each post there are different information but none of them have a definitive answer.
My question is: in my situation is it fine to utilize TPM discarding all summarized gene counts other than those with raw counts > 10 and consider expressend genes with row counts >10? Or it is better to move toward another normalization method like zFPKM to identify the threshold between active and background gene expression?
I'm sorry if this post sounds repetitive with others. I really appreciate any suggestions.
Thank you for your time!