duplicate gene ids after running toxedo protocol

Question

[Kritika]

Hello All I am runnig tuxedo protocol for my human samples after running the cufflink i am getting the duplicate value of gene id and with different fpkms for example

gene id fpkm_control1 fpkm_control2 fpkm_test1 fpkm_test2

abc 0.88 0.65 0.56 0.1

abc 1 0 0 1

I am not able to understand why this duplicate value are coming in my analysis that too with different fpkm values. please help Thanks

[shunyip]

Did you check if they are two isoforms of the same gene?

[Kritika]

They are not isoforms