I am really facing a strong batch effect in my acquired datasets (two batches; 1 and 2). I can see this effect in the three workflows used for analyzing the samples; lipidomics, GC-MS and HILIC-MS. Separation in PCA is strongly related to the batch. I noticed that metaboanalyst has a function for batch correction under MetaboAnalystR package. I am afraid that I don’t have any background in coding and unfortunately couldn’t follow the steps described in the website.
I was wondering if you have other easier tools for normal and not advanced users that can be used for batch effect correction.