Hi, I have run cuffdiff for finding differentially expressed genes in two conditions. Each condition has 3 biological replicates, which were processed using cufflink. The "value_1" and "value_2" columns in gene_exp.diff file don't reflect the FPKM values from cufflinks. The FPKM values from 3 replicates are, 21.168, 39.8954 and 17.9224. But the value_1 for the gene from gene_exp.diff file is 30.3461 (which is definitely not the average of three values) . How does cuffdiff generates 'value_1' and 'value_2' ?
I am using latest versions of cufflink and cuffdiff.
Thanks in advance