pandora Support for PLS-DA/OPLS-DA Models

Metabolomics data is commonly analyzed by PLS-DA and OPLS-DA models. This can be implemented in the R ropls package. Would it be possible to include these model types as options in SIMON? I am curious to compare model performance with the other options already included in SIMON.

Jun 28 '22 02:06 abadgerw

Hi @abadgerw,

Currently there is no OPLS-DA model in SIMON available.

However there are multiple PLS packages available to use in SIMON depending on your system that you may find useful. The pls one should be suitable. Using pls method - partial least squares discriminant analysis (PLSDA) model will be tuned over the number of PLS components that should be retained.

Jun 28 '22 11:06 LogIN-

Thanks! Are there plans to potentially add OPLS-DA models in future versions? The field of metabolomics has really shifted away from PLS-DA to OPLS-DA and would therefore be of use to individuals working with that type of data. However, I'm not sure of how difficult it would be to ultimately implement.

Jun 28 '22 12:06 abadgerw

Hi, you are right. I will add "OPLS-DA" into to-do list for 0.4.0 release milestone.

Jun 28 '22 12:06 LogIN-

Hope all is well! I wanted to see if this had been added yet?

Sep 06 '23 10:09 abadgerw