Dear all,

I am running limma's decideTests on DNA-methylation "M" values, which range from -6 to +6.

The fact that some values are negative leads to my question: How do I interpret the output numbers: -1 and +1? 

Would contrast "A-B" substract the value B from value A?

example: if A = -5 and B= -6 ,

will the contrast "A-B" return (-5)-(-6)=positive (+1)

or return (-5)-(6)= -11 (i.e. negative=-1) ?

One million thanks for any thoughts!

Best, Judith

In the return values from decideTests, the -1 denotes significant down-regulation of a gene while +1 denotes up-regulation.  In your example using -5 and -6, condition A is "higher" in methylation value than condition B, so the resulting decideTests value would be +1.