I am analysing three datasets together (metabolomics, proteomics and phosphoproteomics) and I would like to tune the number of variables I need to include into the block splsda model. However, when I try to tune with tune.block.splsda I get this error:
You have provided a sequence of keepX of length: 10 for block metabolomics and 10 for block proteomics and 10 for block phosphoproteomics.
This results in 1000 models being fitted for each component and each nrepeat, this may take some time to run, be patient!
Error in checkForRemoteErrors(val) :
2 nodes produced errors; first error: Please check the rownames of the data, there seems to be some
I checked the rownames and they are similar between the datasets (namely 1-18). When I was searching for this error I see that this error, or a variation, occurs often (there was a post at this forum as well), but the solution is never really stated. Somewhere it was suggested to use mixOmics 6.11.4 (I now have 6.10.9), but when I try to install mixOmics directly from gitHub, my R is going crazy ( this is not specific for mixOmics, but happens also when trying to download other packages from github). So, my question is whether you know how to solve this error?
This is what I was running:
test.keepX <- list (metabolomics = c(5:9, seq(10, 18, 2)),
proteomics = c(5:9, seq(10, 18, 2)),
phosphoproteomics = c(5:9, seq(10, 18, 2)))
design <- matrix(1, ncol = length(X), nrow = length(X),
dimnames = list(names(X), names(X)))
diag(design) <- 0
tune.TCGA <- tune.block.splsda(X = X , Y = Y, ncomp = 5,
test.keepX = test.keepX, design = design,
validation = ‘Mfold’, folds = 3, nrepeat = 5,
cpus = 2 , dist = “centroids.dist”)
I managed to install a newer version of mixOmics via github (6.11.25), but the problem still persists.