Error in calling tune() or tune.splsda()

Create issue
Issue #72 resolved
Former user created an issue

Using mixOmics 6.1.1, I get the following error when attempting to tune the number of variables to retain on each component in an splsda model. Using the srbct data:

X<-srbct$gene Y<-srbct$class tune<-tune.splsda(X,Y,ncomp=3, folds=5)

0%Error in if (ncol(newx) != p & ncol(newx) != length(A)) { : argument is of length zero

other_tune<-tune(method="splsda",X,Y,ncomp=3,folds=5) Calling 'tune.splsda' | | 0%Error in if (ncol(newx) != p & ncol(newx) != length(A)) { : argument is of length zero

I'm not sure I understand the nature of this error. In the above data, dim(X)[1]==length(Y).

Comments (4)

  1. Florian Rohart

    Hi There,

    This seems to be a clash with another package because there is no "newx" string in any of the mixOmics code. I would imagine that restarting R, and only loading mixOmics and the srbct data would do the trick.

    Please advise whether this is working

  2. tjgross

    Florian, Thank you for for the help. It appears that there was indeed a clash with another package. Both tune.splsda and the tune wrapper function are working appropriately now for discriminant analysis.

    However, when I move over to using the tune wrapper to choose the number of variables to retain on each component of a sPLS model, I get the following:

    X <- liver.toxicity$gene Y <- liver.toxicity$clinic tune<-tune(method="spls", X=X, Y=Y, ncomp=2,folds=5, nrepeat=100)

    Calling 'tune.multilevel' with method = 'spls' Error in tune.multilevel(X = X, Y = Y, multilevel = multilevel, mode = mode, : argument "multilevel" is missing, with no default

    I understand this pertains to tuning a multilevel model for repeated measurements. I am unsure what to supply in the given case, where data are representative of only one time point.

  3. Kim-Anh Le Cao repo owner

    Hello, The tune does not apply for a sPLS method (as it is a bit tricky to tune). We'll fix that in the next update. Best is to use the function perf that measures the performance of sPLS in a multivariate context. See example in ?perf

  4. Log in to comment