when I perform SAM analyses in TMEV, the x-coordinates (expected) I see on the SAM graph do not match with the data in Table View.
I find - for instance - a gene with coordinates in the SAM graph (1.57; 2.88). In Table View the observed score (d) is fine (2.88) but the expected score (dExp) is only 0.33. For some other genes the expected score is negative and the observed score has a positive value (which seemed weird to me). However, this 'outlying' x-value 1.57 is present in the list, but assigned to another (housekeeping) gene.
Do I have to multiply or divide dExp by a certain factor to become the values I see in the SAM graph? Are the values in Table View shifted? Is someone else having this problem?
I work with MeV_4_8 and experience the same problem on Mac OS X and Windows XP.
All advice is welcome.
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