Problem using Phenoigraph Clustering with bigger data sets

[MalteLehmannn]

Hi,

I am experiencing an issue trying to use the Phenograph algorithm on bigger datasets. I have a set of three cohorts containing 10, 12 and 15 samples (each a 1 mm core). I computed a tSNE with some of the markers. If I run the Phenograph algorithm for any smaller subset of the samples it works. If, however, I try to run it on all the samples or a larger subset, HistoCAT breaks down. I installed MathLab to see the error message and it reads the following (see below).

Is their any way to run larger sample sets?

In LouvainfromBin_Windows>cleanup (line 109)
In LouvainfromBin_Windows (line 82)
In phenograph (line 73)
In Run_Phenograph_Callback (line 37)
In analyze_button_Callback (line 80)
In gui_mainfcn (line 95)
In histoCAT (line 42)
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject))
Warning: File 'G.tree' not found.

In LouvainfromBin_Windows>cleanup (line 109)
In LouvainfromBin_Windows (line 82)
In phenograph (line 73)
In Run_Phenograph_Callback (line 37)
In analyze_button_Callback (line 80)
In gui_mainfcn (line 95)
In histoCAT (line 42)
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject))
Warning: File 'G_graph.weights' not found.
In LouvainfromBin_Windows>cleanup (line 109)
In LouvainfromBin_Windows (line 82)
In phenograph (line 73)
In Run_Phenograph_Callback (line 37)
In analyze_button_Callback (line 80)
In gui_mainfcn (line 95)
In histoCAT (line 42)
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject))
Warning: File 'G.bin' not found.
In LouvainfromBin_Windows>cleanup (line 109)
In LouvainfromBin_Windows (line 82)
In phenograph (line 73)
In Run_Phenograph_Callback (line 37)
In analyze_button_Callback (line 80)
In gui_mainfcn (line 95)
In histoCAT (line 42)
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject))
Warning: File 'G_graph.bin' not found.
In LouvainfromBin_Windows>cleanup (line 109)
In LouvainfromBin_Windows (line 82)
In phenograph (line 73)
In Run_Phenograph_Callback (line 37)
In analyze_button_Callback (line 80)
In gui_mainfcn (line 95)
In histoCAT (line 42)
In matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject))
assigning random number for current Phenograph
Unable to perform assignment because the size of the left side is 377220-by-1 and the size of the right side is 197709-by-1.

Error in addChannels (line 76)
sessionData(gate_context, last_def_channel+1:last_def_channel+size(new_data, 2)) = new_data;

Error in Run_Phenograph_Callback (line 50)
[sessionData,gates] = addChannels(new_channel_name, new_data, opt_gate_context,opt_gates, gates, sessionData);

Error in analyze_button_Callback (line 80)
Run_Phenograph_Callback;

Error in gui_mainfcn (line 95)
feval(varargin{:});

Error in histoCAT (line 42)
gui_mainfcn(gui_State, varargin{:});

Error in matlab.graphics.internal.figfile.FigFile/read>@(hObject,eventdata)histoCAT('analyze_button_Callback',hObject,eventdata,guidata(hObject))

Error while evaluating UIControl Callback.