Principal component analysis

RNA-Seq with Bioconductor in R

Mary Piper

Bioinformatics Consultant and Trainer

PCA example

Principal component analysis (PCA): Theory

pca 2sample

Principal component analysis (PCA): Theory

pc2

Principal component analysis (PCA): Theory

PC influence

Principal component analysis (PCA): Theory

PCA influence

Principal component analysis (PCA): Theory

PCA influence

Sample1 PC1 score = (4 * -2) + (1 * -10) + (8 * 8) + (5 * 1) = 51
Sample1 PC2 score = (4 * 0.5) + (1 * 1) + (8 * -5) + (5 * 6) = -7 

Sample2 PC1 score = (5 * -2) + (4 * -10) + (8 * 8) + (7 * 1) = 21
Sample2 PC2 score = (5 * 0.5) + (4 * 1) + (8 * -5) + (7 * 6) = 8.5

PCA sample values

pca example

Principal component analysis (PCA): Theory

# Plot PCA 
plotPCA(vsd_wt, intgroup="condition")

pca_DESeq2

Let's practice!

RNA-Seq with Bioconductor in R