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Omicsoft is the leading provider of Next Generation Sequencing, Cancer Genomics, Immunology, and Bioinformatics solutions for Next Generation Sequencing Data and Gene Expression Analysis.

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Keeping you up-to-date with the latest in NGS, Bioinformatics Analysis, and cancer genomics with blogs on Array Suite, OncoLand (TCGA and more), ImmunoLand, and more.

[New Feature] Improved Visualization: PCA Ellipse

Vivian Zhang

Principal components analysis (PCA) is commonly used for clustering gene expression data. It allows us to cluster genes based on the different conditions, such as treatment and control, drug responses, time points etc. With new Array Suite 9.0 release, we improve our PCA visualization by adding PCA ellipse to display PCA confidence level. 

 

As an example, let's look at the gene expression data from two different case and control groups. A 2D PCA on the dataset: 

2D PCA on case vs control dataset. There are three ellipses representing 3 confidence regions: The black ellipse for all samples, the blue ellipse for case samples and the green ellipse for control samples.  

2D PCA on case vs control dataset. There are three ellipses representing 3 confidence regions: The black ellipse for all samples, the blue ellipse for case samples and the green ellipse for control samples.  

The confidence level indicated by the ellipse helps user to better "visualize" the confidence of the clustering.