opt-SNE datasets

Data files referenced within the opt-SNE preprint (https://doi.org/10.1101/451690) are available for download below
Flow18parameter
18 parameter fluorescent flow cytometry file from http://doi.wiley.com/10.1002/cyto.a.22983.
flow18_annotated.fcs - an FCS file with all original channels. An extra channel is included that identifies cell types assigned by expert gating. The data are compensated and all fluorescent parameters scaled by the function asinh(x/150).
flow18_for_optsne.csv - the data from above but converted to a CSV file that can be used as input to the open-source Multicore-opt-SNE package. Only channels used for opt-SNE analysis are included in the file. Note that the events are sorted by class ID, so if subsetting the file it is recommended to randomize the row order beforehand.

tsne_results_flow18.csv - an example of opt-SNE results for the Flow18parameter dataset.
Mass41parameter
41 parameter mass cytometry dataset from https://doi.org/10.1126/science.1198704.
mass41_annotated.fcs - an FCS file produced by concatenation of multiple files from the original dataset. An extra channel is included that identifies cell types assigned by expert gating. An additional extra channel identifies file of origin. All mass parameters are scaled by the function asinh(x/5).
mass41_for_optsne.csv - the data from above but converted to a CSV file that can be used as input to the open-source Multicore-opt-SNE package. Only channels used for opt-SNE analysis are included in the file. Note that the events are sorted by class ID, so if subsetting the file it is recommended to randomize the row order beforehand.
tsne_results_mass41.csv - an example of opt-SNE results for the Mass41parameter dataset.