I have a question regarding the default parameters for OPLS-DA plots, specifically for cross-validation. I saw in the MetaboAnalystR package that the default cross-validation for the opls function was 7-fold, and that the number of samples (rows in ‘x’) has to be at least more than or equal to the cross-validation number.
In my dataset, I have 3 samples per treatment group, so a total of 6 samples. I was able to generate an OPLS-DA plot after setting the cross-validation to 6. My question is this – what does the web app version do? Does it default to the maximum number of rows (i.e. samples)? I have been able to run my data through the web application and generated the same OPLS results, but I was curious about these settings in the web app results and wanted to be sure.
Many thanks in advance!