how does mavolcanoplot calculate fold changes? (dumb question?)

I want to know how exactly the fold changes are calculated by mavolcanoplot(). It seems that the fold changes are not something simple like mean(Yreplicates)/mean(Xreplicates), at least not by my inspection of the input DataMatrix arrays. I assume it has to do with the p values that are used as input, but I don't see how.

Also, I assume a fold change of say +2.2 for a particular gene with inputs X and Y means that Y's expression of the gene is 2.2 times more than X's expression of the gene. If the fold change is -2.2, then Y's expression is 2.2 times less than X's expression. If this is the case (hopefully!) the documentation of the output argument should clarify this explicitly, but it does not. I don't have this backwards do I?

thanks in advance

Answer 1

[Syed Wafa]

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