Which method is more suitable for RNA extraction from FFPE tissues from breast cancer patients, since Trizol-based method is giving lower absorbance while kit-based method is lowering the conc. but purity wise, it is better.

Moreover, is there any chance if inhibition to PCR amplification due to the fixation of the tissues or later on by extraction processes. Since I have been facing troubles with real-time PCR using this samples as most commonly used genes GAPDH and B-Actin are not giving appropriate amplification values. Do I need to try some other house-keeping genes for that purpose or is the quality of sample is compromised already.