[galaxy-user] cuffdiff: same gene listed with different FPKM values

Dear all, has anything like this happened to you?

I compared two samples with cuffdiff and when I look at the differentially expressed genes values I have the same gene listed for 5 times with different values.

E.g. sample1 sample2 gene 71.6837 9.76435 NM_005514 87.6456 27.3965 NM_005514 115.333 4.81687 NM_005514 38.1879 5.2753 NM_005514 69.4197 5.84387 NM_005514 112.964 3.89226 NM_005514

What does this mean? And how do I know which one represents the real expression level for that gene for the two samples?

Thanks, ib