[galaxy-user] Cuffdiff output

Hi, I have a question about interpreting the cuffdiff data and how to pick up significant genes. I have genes which show ~8 fold change between 2 conditions: eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is threshold of FPKM below which Cuffdiff does not consider it an FPKM to be valid and hence significance in "no"? What downstream analysis should I use to extract a meaningful list of genes from the Cuffdiff data?

Also, I filtered out FPKMs which were below 5 in both conditions? Is that reasonable?

Thanks Shivani