I have qPCR data samples with a lot of noise and a general low amplification. Many Ct values are set therefore to 40 (or NA, I'm using R package HTqPCR). My question is whether I should filter out "genes where the results are of low quality" before performing DE analysis, and how I can trust the p-values. Are results not going to be misleading if I significant fraction of the genes is removed from the analysis?
Thanks in advance