Question about batch effects in refine.bio datasets

Hi!

I am trying to understand whether batch effects are corrected for in the refine.bio pipeline.

I downloaded the dataset GSE99039 (microarray) from refine.bio then looked at the dataset using PCA. I noticed that the dataset from refine.bio seem to have a clear separation that does not match any of the metadata.

refine.bio PCA

Hence would like to ask about
i. where is the part in the pipeline that does the (quantile?) normalization
ii. i understand that for the normalized data pipeline if any batch correction was performed.

Thank you.

No file, test, or entry point is named. Start by locating the refine.bio normalization and batch-correction documentation or pipeline entry point for GSE99039, then document whether each step is applied and where it occurs.

Written by the indexing model from the issue text.