Using the last version, which also gives fold changes for the two-class analysis using SAM, I was surprised to see that, for negative d-scores, the fold change values were positive. In fact, all the changed genes, whether they had positive or negative d-scores, had always positive fold changes values. Can anyone help please with this? Thank you.
Fold change is a ratio calculation, and thus should not have negative values. For example, a perfectly flat expression between treatment and control would result in a fold change of 1.0.
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