Vignette 5.8.5 - Error?

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Hi Al,

Thank you for your help!

Using the mixOmicsTeam GitHub vignette instead of the mixOmics website vignette allowed me to plot the perf results successfully, although it is still different to the one in the vignette:

plot(perf.pls, criterion = 'Q2.total'

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I’ve managed to get the tune plot working as well, but it comes with the warning:

Warning message:
The SGCCA algorithm did not converge

Which I’ve read about and seems to suggest the number of components is too large (The SGCCA algorithm did not converge and length of variable selection)?

Trying to reduce the number of components seemed to have no impact, and the resulting plot is quite different to the one in the example vignette (on the website):

#This code is from the GitHub Vignette
tune.spls.cor <- tune.spls(X, Y, ncomp = 3,
                           test.keepX = list.keepX,
                           validation = "Mfold", folds = 5,
                           nrepeat = 10, progressBar = FALSE,
                           measure = 'cor')
#Which returns the error "The SGCCA algorithm did not converge"

plot(tune.spls.cor, measure = 'cor')

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If I then ran the code for the optimal number of variables:

tune.spls.cor$choice.keepX

Then I get:

comp1 comp2 comp3 
    2     2     2

Compared with:

# comp1 comp2 comp3 
#    15     3    20

In the vignette, so it seems like it still isn’t quite working for me.

Thanks again for helping out.

Kind regards,
Sam