The above error keeps popping every time I try to do batch correction for my metabolomics samples. I ran my samples using LC-MS and annotated the samples from different batches together at Compound Discoverer 3.0. But since PCA and PLSDA both show distinct clusters strongly suggesting batch-effect error I wish to perform the batch correction but I think the tool is not working for my samples. Is it because I have too many metabolites (3530) or samples (112)???
I had this error myself. This is a formatting error. You need to format your dataset exactly as the template.E.g. transform your annotate peaks to Feature01 etc., add letters for classes etc.
Georgia