plotVar components are not orthogonal with NA values

Analysis
1

Hello,
When I use the function the function block.splsda for integration, it seems that the components are not orthogonal for a block when this block contains NA. I would like to know how can I interpret the correlation circle in this case.
Best regards

Maxime

2

Hi Maxime,

Did you recalculate the crossproduct between components to assess orthogonality? (just curious!)

Missing values are a problem, often in a plotVar the variables may happen to be outside the circle! Two options:

  • filter out the variables with too many missing values
  • impute prior to the analysis: either with NIPALS (we give an example in our website www.mixOmics.org) or some other technique.

Hope that helps,

Kim-Anh