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.

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?

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