Methodology article
Data reduction for spectral clustering to analyze high throughput flow cytometry data
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* Corresponding author: Ryan R Brinkman rbrinkman@bccrc.ca
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 2010Additional files
Additional file 1:
Report on identification of rare population. The table contains the full detailed report on our comparative experiment for identifying rare populations.
Format: XLS Size: 15KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 2:
High dimensional flow cytometry data. This data file contains a matrix with 100,000 rows and 23 columns that represents a flow cytometry sample with 100,000 events. It can be directly loaded in R and analyzed by SamSPECTRAL. It takes less than 12 minutes to perform faithful sampling on this 23 dimensional data.
Format: RDAT Size: 7.1MB Download file
Additional file 3:
Parameters for GvHD data set. These values are appropriate for running SamSPECTRAL on GvHD data set.
Format: ZIP Size: 219KB Download file
Additional file 4:
Parameters for stem cell data set. These values are appropriate for running SamSPECTRAL on stem cell data set.
Format: ZIP Size: 32KB Download file
Additional file 5:
Parameters for telomere data set. These values are appropriate for running SamSPECTRAL on telomere data set.
Format: ZIP Size: 163KB Download file
Additional file 6:
Parameters for viability data set. These values are appropriate for running SamSPECTRAL on viability data set.
Format: ZIP Size: 15KB Download file
Additional file 7:
Simulation with synthetic data. This R source code produces synthetic data with 5 clusters shown in Figure 5. The resulting data is passed to SamSPECTRAL to be clustered.
Format: R Size: 2KB Download file