[galaxy-dev] cuffdiff output: FPKM value zero

Hello everyone,

I am comparing two samples (control and treated) paired end RNA Seq data. In the cuffdiff output I have noticed that few genes have zero FPKM value in one sample and other sample has significant FPKM value. I want to identify uniquely expressed genes identified only in one sample (either control or treated).

My question: If something is measured with significance in one sample (high FPKM), but not measured at all in another sample (Zero FPKM), should I consider that gene as significant?

Can anyone explain this.

Thanks

suz