I have analyzed methylation data using mixOmics. Methylation signal obtained with RRBS technic consists in a methylation percentage for each CG genomic position studied. Therefore, the methylation is always positive.
After having applied a SPLS/DA, I wanted to visualize selected variables using cim function. I was quite astonished to see a color scale gradient starting at a negative value.
I tried to use scale parameter (TRUE/FALSE), but it had no effect : the gradient still started at a negative value.
I realized (with the help of S.Dejean) that scale parameter in splsda has TRUE for defaut value. Therefore, I got a scaled matrix after having applied splsda and when I pass it to cim, the scale parameter of this function has no more effect.
Can you confirm this interpretation ?
Thank you in advance