Methodology article
Data reduction for spectral clustering to analyze high throughput flow cytometry data
1 Department of Computing Science, University of British Columbia, Vancouver, BC, Canada
2 Terry Fox Laboratory, BC Cancer Agency, 675 W 10th Ave., Vancouver, BC, Canada
3 Faculty of Science, University of British Columbia, Vancouver, BC, Canada
4 Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
BMC Bioinformatics 2010, 11:403 doi:10.1186/1471-2105-11-403
Published: 28 July 2010Abstract
Background
Recent biological discoveries have shown that clustering large datasets is essential for better understanding biology in many areas. Spectral clustering in particular has proven to be a powerful tool amenable for many applications. However, it cannot be directly applied to large datasets due to time and memory limitations. To address this issue, we have modified spectral clustering by adding an information preserving sampling procedure and applying a post-processing stage. We call this entire algorithm SamSPECTRAL.
Results
We tested our algorithm on flow cytometry data as an example of large, multidimensional data containing potentially hundreds of thousands of data points (i.e., "events" in flow cytometry, typically corresponding to cells). Compared to two state of the art model-based flow cytometry clustering methods, SamSPECTRAL demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations.
Conclusions
This work is the first successful attempt to apply spectral methodology on flow cytometry data. An implementation of our algorithm as an R package is freely available through BioConductor.
