I am using DIABLO to integrate two different omics datasets in a supervised manner. However, when I am ‘creating’ my design with the code:
pls.res ← pls (X,Y, ncomp = 1)
I get the following warning message:
In cor(A[[k]], variates.A[[k]] : the standard deviation is zero
I got this warning message also when using two other datasets. The correlation between the datasets is usually really high (like 0.95). And I get this warning with the block.splsda code as well. I do get, as far as I can judge, good models as outcome. Is this warning message a problem? Could this be a problem of pre-filtering the datasets (as is suggested in: Filtering large data to use with DIABLO)? I do not get the warning when using the breast.TCGA dataset, so it is not my machine/laptop (I suspected that first). I also think the number of components is not the problem (as suggested in: Integration with genotype data) since I already get the warning with 1 component.
Then I had another question about the DIABLO tuning (with the perf function). When I do this with the two datasets (the first ones I mentioned). I get the error: r in '.rowNamesDF ← '(x, value=value) : missing values in 'row.names’are not allowed. But the rownames are specified and I use the exact same code as I have used before, so I dont know what is going wrong here. Can you help?