Error when running tune.block.splsda

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Issue #126 resolved
Marc created an issue


I'm running DIABLO script for a combination of microbiome and metabolomics datasets, using the last mixOmics package version available in CRAN. I managed to make it work until the tunning step. When I run the code (as is written in the original script) it returns me the following error:

set.seed(123) # for reproducibility
test.keepX = list (Metab = c(5:9, seq(10, 18, 2), seq(20,30,5)),
                   Micro = c(5:9, seq(10, 18, 2), seq(20,30,5)))
t1 = proc.time() = tune.block.splsda(X = data, Y = Y, ncomp = ncomp, 
                       test.keepX = test.keepX, design = design,
                       validation = 'Mfold', folds = 10, nrepeat = 1, dist = "centroids.dist", cpus=4, = T)

Error in checkForRemoteErrors(val) : 
  4 nodes produced errors; first error: Each 'newdata[[i]]' must include all the variables of 'object$X[[i]]'

I don't know if maybe I should change the test.keepX construction? Either way, I don't know what it really does and if it should be specific for each data type.

Thanks for the help in advance :)

Comments (2)

  1. Florian Rohart

    Hi Marc,

    I think I found the bug you mentioned. The next release should fix it. If you send me an email I can send you the fix and you can try it out!


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