Thanks again for the wonderful
mixOmics package and
DIABLO. In another project where I am integrating mRNA (~3000), protein (~1300), and metabolites (~160) across 31 samples, I am finding some issues with selected features from the metabolites panel that is discriminating my categorical outcome.
I ran DIABLO using
list.keepX with a full design. This
list.keepX was obtained using
tune.block.splsda function as below.
test.tune.BBM = tune.block.splsda(X = data, Y = Y, ncomp = 2,test.keepX = test.keepX, design = design2, validation = 'Mfold', folds = 5, nrepeat = 1,dist = "centroids.dist") list.keepX # $mRNA #  30 5 # $protein #  14 16 # $metabolite #  9 5 MyResult.diablo.tune <- block.splsda(X, Y, keepX=list.keepX,design = design2) > metabolite.c1$metabolite$value value.var Cystine -0.5932985 citrulline -0.4469610 succinate -0.4053713 Hydroxyphenylacetic.acid -0.3018932 fructose.6.phosphate -0.2679044 Hydroxyisocaproic.acid -0.2487210 S.adenosyl.L.homoCysteine -0.1651630 arginine -0.1488625 myo.inositol -0.0984053 > metabolite.c2$metabolite$value value.var anthranilate -0.68325915 trehalose.sucrose -0.62615245 Mevalonic.Acid -0.27213253 fructose.6.phosphate -0.25845751 dGTP -0.01528562
Now when I
fructose.6.phosphate is showing up twice in both the components in the metabolite data with different
value.var. This has not happened earlier with other projects. Can you give some inputs as to why this is happening and how to explain this issue?