I have a question: I did transcriptome analysis on a cassava genotype harvested at 24 hr and 72 hr, compared with non-infested healthy plants. I had 3 biological replicates for each time-point, analysed with tophat/cufflinks/cuffdiff. The 3 biological replicates RNA-seq data from the cufflinks was used to test correlation on R and on excel between the replicates, however, I get a negative correlation, because there is a high difference in the FPKM values. Can you advise as to how I can calculate correlation between the replicates?
OR any other method?