I was using cuffdiff 1.3.0 to compare four BAMs aligned with TopHat 1.4.1. I have noticed that zero FPKM values are never considered significant when compared with large FPKM values. Here is one example that I am concerned about:
XLOC_017834 XLOC_017834 Olfr1307 2:111784672-111785611 FF FMC OK 0.257545 46.5301 7.4972 -4.50075 6.77156e-06 0.000658507 yes XLOC_017834 XLOC_017834 Olfr1307 2:111784672-111785611 FFC FMC OK 0 46.5301 1.79769e+308 1.79769e+308 0.0789649 0.365761 no XLOC_017834 XLOC_017834 Olfr1307 2:111784672-111785611 FM FMC OK 0.0380371 46.5301 10.2565 -5.37179 7.79602e-08 2.39776e-05 yes
If line wrapping destroys the above genesexp.diff output, here is a brief summary: FMC has an FPKM of 46.5301 and when compared to FF (FPKM=0.257545) and FM (FPKM=0.0380371) the q-value is below the FDR of 0.05. Appropriately the significance value is labeled as 'yes'. However, FFC has an FPKM of zero and this differential test is not significant. The goal of the experiment was to identify uniquely expressed genes only identified in the FMC data set. As such an infinite log(foldchange) seems more significant than the other comparisons. Can anyone explain this?