Hi,
I am currently working on a multi-omics analysis using Multi-block sPLS-DA with 5 datasets using the following code, where ‘design’ is a full-weighted design.
list.keepX <- data.frame(
Urine = c(5, 5, 5, 10, 15),
Blood = c(13, 3, 3, 3, 3),
Fecal = c(15, 20, 25, 25, 10),
CSF = c(15, 5, 10, 5, 5),
Plasma = c(10, 10, 5, 5, 5)
)
adjusted_MB_splsda <- block.splsda(X, Y, ncomp = 5,
keepX = list.keepX, design = design)
circosPlot(adjusted_MB_splsda, cutoff = 0.8, line = TRUE, comp = 1,
size.variables = 1, size.labels = 1.2, size.legend = 1,
color.blocks = c("#999999", "#E69F00", "#56B4E9", "#009E73", "#ffcad4"),
color.cor = c("chocolate3","grey20"))
network(adjusted_MB_splsda, cutoff = 0.8,
color.node = c("#E69F00", "#56B4E9"),
save = 'pdf', name.save = 'images/MO_diablo-network_5D')
I have a few questions regarding the results:
-
Why do the network and circosPlot show different variables with the same cutoff selected? I believe the default blocks for network is (1,2), so (Urine, Blood), but the metals (blood) in the network don’t show up as a line in the circosPlot?
-
I’m working on data from a twin study, do I have to adjust for this in the analysis? And is there a way to test for/display variance ‘within pairs’ and ‘between pairs’ using their twin_id?
-
Is there a way to test for an association between the results and clinical phenotypes?
Thank you so much in advance for helping and making this amazing package!