Hello:
I am a new user for the DIABLO. I am working with DIALBO to integrate two different omic datasets. Could you guide me to find how to set the right ncomp for block.splsda?
In addition, I have a naive question regarding the circosPlot. How the ncomp in block.splsda function affects the output?
Thanks in advance for your patience and help.
Best wishes
Kai
hi @Kai,
Choosing the number of components in DIABLO can be done using the tune function of a non sparse DIABLO model. This is described here: http://mixomics.org/mixdiablo/case-study-tcga/
The circosPlot will show all the variables selected on each of the components, so if you specify comp = 1, then you will see a set of variables selected on component 1. By default it is set to all components (say comp = c(1:3) if you have 3 components): ask variables selected across all 3 components will be shown. You can also specify specific components to plot in that function, e.g. comp = 2.
Kim-Anh