Question: Limma -decideTests interpretation for M-values
1
gravatar for kraiczy
3.6 years ago by
kraiczy10
kraiczy10 wrote:

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

 

 

limma methylation decidetests • 730 views
ADD COMMENTlink modified 3.6 years ago by Sean Davis21k • written 3.6 years ago by kraiczy10
Answer: Limma -decideTests interpretation for M-values
2
gravatar for Sean Davis
3.6 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:

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.   

ADD COMMENTlink written 3.6 years ago by Sean Davis21k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 197 users visited in the last hour