I recently discovered mixOmics and have tried to use PLS-da on my data set consisting of methylation percentages for cytosine sites among different groups, so what I have is a matrix of 27 samples and 440 000 sites.
The initial output of PLSDA() works fine, but when I try to do assess performance with perf(), I get the error message:
Error in solve.default(Sr) : **
** system is computationally singular: reciprocal condition number = 8.57685e-18
I initialy thought, by reading some comments here, that I used to many components in the initial PLSDA()-call, but I also read that to similar values of the different variables(?) might cause this error message to occur. I know from PCA that there is very little variation between the different groups in my data, meaning that the percentage-values might be very similar for each variable across all samples.
Could this be the reason I get this error message or is there something else I need to consider?