PCA

permutation test for PCA components

PCA is a critical method for dimension reduction for high-dimensional data. High-dimensional data are data with features (p) a lot more than observations (n). However, this is changing with single-cell RNAseq data. Now, we can sequence millions (n) of single cells and each cell has ~20,000 genes/features (p). I suggest you read my previous blog post on using svd to calculate PCs. Single-cell expression data PCA In single-cell RNAseq analysis, feature selection will be performed first.

PCA in action

PCA in practice. Principle Component Analysis(PCA) is a very important skill for dimention reduction to analyze high-dimentional data. High-dimentional data are data with features (p) a lot more than observations (n). This types of data are very commonly generated from high-throuput sequencing experiments. For example, an RNA-seq or microarry experiment measures expression of tens of thousands of genes for only 8 samples (4 controls and 4 treatments). Let’s use a microarray data for demonstration.