Hi, I am wondering anyone has information on the batch effects correction on these scRNAseq data? According to the Wiki and the paper (https://www.biorxiv.org/content/10.1101/2023.03.07.531493v1.full.pdf), it says "The following pipeline was executed on the RNA count matrix: normalization and scaling by SCTransform method (with variable.features.n=2000, conserve.memory=T, Seurat package version 445), dimensionality reduction by PCA (Seurat RunPCA, npcs=30), construction of k-NN neighbor graph (Seurat FindNeighbors, dims=1:30) and Louvain community detection clustering (Seurat FindClusters, resolution=0.2, algorithm=1)." There is nothing about how to combine the 60+ batches from the read counts off cell ranger. Is seurat IntegrateLayers() or other tool used? Or the count matrices from different batches were simply combined? I did try to search but failed to find the information. Thank you very much! Li

Created by Li Sun rikku1983
@masashi Would you be able to help answer this question about how the count matrices for the most recent 465 ROSMAP snRNAseq samples were combined? Thanks! Abby
Hi Li, I'm sorry to hear that you weren't able to find the information you need in the preprint, or in the study description Wiki content. The author of the paper and contributor of the data, @gilad.green, should be able to answer your question. Regards, Jessica

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