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Pancreas4_Data.Rmd
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Pancreas4_Data.Rmd
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---
title: "Pancreas 4 Data"
author: "Kevin Wang"
date: "`r paste0(format(Sys.time(), '%d %b %Y'))`"
output:
html_document:
theme: paper
toc_depth: 3
number_sections: yes
toc: true
---
## Introduction
This is a human pancreas single-cell data comprising of 4 experiments.
**Integration challenge**
+ Prior to integration, there is a strong separation effect by experiments.
+ In addition, there are 3 different protocols, the sequencing depths poses an extra challenge.
+ With 4,566 cells, this data poses a moderate 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 |
|----------------------------------------------------|---|-----------|-------------|-------------|----------------------------|------------|----------|----------|-----------------|------------|--------------|
| Across platforms with significant depth difference | | Pancreas4 | GSE81608 | Xin | 10.1016/j.cmet.2016.08.018 | SMARTer/C1 | Human | Pancreas | 6 | 4566 | NA |
| | | | GSE83139 | Wang | 10.2337/db16-0405 | Smart-Seq | | | | | |
| | | | GSE86469 | Lawlor | 10.1101/gr.212720.116 | SMARTer/C1 | | | | | |
| | | | E-MTAB-5061 | Segerstolpe | 10.1016/j.cmet.2016.08.020 | Smart-Seq2 | | | | | |
+ Relation to the `scMerge` article: Supplementary Figure 4 and 5.
## Data visualisation
### PCA plots by cell types and batch
![](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scMergeWebsite/Pancreas4_Data/FigS4_v1.png){width=100%}
### RLE plots and percentage of explained variance plots
![](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scMergeWebsite/Pancreas4_Data/FigS5_v1.png){width=100%}
## Integrated `scMerge` data
+ Data availability: [Pancreas4 (in RData format)](http://www.maths.usyd.edu.au/u/yingxinl/wwwnb/scMergeData/pancreasFour_scMerge.rds)
+ `scMerge` parameters for integration:
- Unsupervised scMerge
- kmeans K = (4,6,6,6)
- Negative controls are human scSEG