How cufflinks handles the genes whose expression values varies a lot among biological replicates. If it takes into account, is it averaged then or what? Also, imagine a case when the fold change between biological replicates is bigger than the conditions to compare?
Another question is, why the same gene in the same condition is having slightly different RPKM values in different lists? Consider, comparing condition A and B, gene X has RPKM=23 and condition A and C, same gene X of A has RPKM=22.5.
P.S. I think I need to study more about cufflinks.