I will soon start working with RNA-seq for analyzing gene expression for patient groups. I understand that having both technical and biological replicates are important in designing a RNA-seq experiment. Since I will mostly be analyzing samples from healthy and diseased individuals, I don't think I will have any technical replicates as the samples are from different individuals and sequenced separately. Is it safe to say that I will have 9 biological replicates per condition, assuming that I have 10 individuals from each group?
Also, I was going through the cuffdiff documentation, could somebody please explain how the p-value is calculated for the gene-expression file?