Unexpected result in plotVar comparatively to the optimized sPLS I performed

Hi everyone,

My project is about predicting, with transcriptional data (X), a disease severity score (Y).
I performed an sPLS that I optimize with the perf function.
The final 25 genes I have in my 2 first components seem to well represent the severity score in plotindiv function.

But when I performed plotVar function, my variables don’t look strongly correlated to my severity score.

Is there something I don’t understand or I did not do well in my analyses ?

Thanks a lot for your help.
Alain

dear @alain_LU,

The plotVar coordinates represent the correlation between each original variable, and its associated component. It might be worthwhile to check first the correlation between the components associated to X and Y to see if they strongly agree (for example with a scatter plot). Also remember that the correct interpretation should be ‘a linear combination of the selected variables is correlated with the severity score’, not individual variables themselves.

Hope that helps,

Kim-Anh