Breast Cancer Data

Kevin Wang

12 Apr 2024

Source: vignettes/case_study/Breast_Data.Rmd

Introduction

This is a human breast cancer single-cell data comprising of 4 different batches from a single experiment.

Integration challenge

  • Prior to integration, there is a strong separation effect by batches.
  • With 24,520 cells, this data poses dimensionality challenge to data integration.

Data description

  • Data source:
Type of merge Name ID Author DOI or URL Protocol Organism Tissue # of cell types # of cells # of batches
Within experiment Breast GSE113197 Nguyen 10.1038/s41467-018-04334-1 10x Chromium Human Breast cancer 3 24520 4
  • Relation to the scMerge article: Supplementary Figure 7.

Data visualisation

tSNE plots by cell types and batch

Integrated scMerge data

  • Data availability: Breast Data (in RData format)

  • scMerge parameters for integration:

    • Unsupervised scMerge
    • kmeans K = (4,3,4,3)
    • Negative controls are human scSEG