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 


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