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Table of Contents

Flow Cytometry for Lab 6 ................................................ ................................................... 1

DATA IMPORT ....................................................................... ......................................... 1

SSC versus FSC ..................................................................... ............................................ 1FL-1 versus FL-2 ............................................................................ ................................... 2

References ........................ ....................................................... .......................................... 3

Flow Cytometry for Lab 6clc; close all; clear all;

DATA IMPORTRequest the numeric data, text, and a copy of the unprocessed (raw) data from the Excel file in the first

example.

[data, params, alldata] = xlsread('Calcein and EHD ROS 25-1.001 new.xlsx');

SSC versus FSCA histogram of one parameter is one way to look at the data. hist(data,xvalues): where data is the number

of times the single value of xvalues occured. Scatterplot colored by density function dscatter obtained

from [3].

% FSC

figure (1)

subplot(2,2,1)

hist(data(:,1),max(data(:,1)));

view([-90 90])

grid

title(params(1));

xlabel(params(1));

ylabel('frequency');

% SSC

subplot(2,2,4)

hist(data(:,2),max(data(:,2)));

set(gca,'YDir','reverse');

grid

title(params(2));

xlabel(params(2));

ylabel('frequency');

% FSC vs. SSC

subplot(2,2,2)

%scatter(data(:,1),data(:,2),'.','b') this way doesn't show density

dscatter(data(:,1),(10.^(data(:,2)/256))./10,'log',true)

hold on

dscatter(data(:,1),(10.^(data(:,2)/256))./10,'log',true,'plottype','contour'

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hold off

grid

title('FSC vs. SSC');

xlabel(params(1));

ylabel(params(2));

FL-1 versus FL-2

Hline and Vline functions obtained from [1]

% For FL-1 vs. FL-2

tl = 0; tr = 0; bl = 0; br = 0;

fori=1:1:10000

if(data(i,3)>=10 && data(i,4)>=10)

tr = tr+1;

elseif(data(i,3)=10)

tl = tl+1;

elseif(data(i,3)

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dscatter(data(:,3),(10.^(data(:,4)/256))./10,'log',true)

hold on

dscatter(data(:,3),(10.^(data(:,4)/256))./10,'log',true,'plottype','contour'

vline(10,'g')

hline(10,'g')

hold off

gridtitle('FL-1 vs. FL-2');

xlabel(params(3));

ylabel(params(4));

set(text(5,25,num2str(tl/100)), 'rotation', -90)

text(25,25,num2str(tr/100))

text(25,5,num2str(br/100))

set(text(5,5,num2str(bl/100)), 'rotation', -90)

References

[1] http://www.mathworks.com/matlabcentral/fileexchange/1039-hline-and-vline

[2] Paul H. C. Eilers and Jelle J. Goeman, Enhancing scatterplots with smoothed densities, Bioinformatics,

Mar 2004; 20: 623 - 628.

[3] http://www.mathworks.nl/matlabcentral/fileexchange/8430-flow-cytometry-data-reader-and-visual-

ization/content/html/facsdemo.html

http://www.mathworks.nl/matlabcentral/fileexchange/8430-flow-cytometry-data-reader-and-visualization/content/html/facsdemo.htmlhttp://www.mathworks.nl/matlabcentral/fileexchange/8430-flow-cytometry-data-reader-and-visualization/content/html/facsdemo.htmlhttp://www.mathworks.com/matlabcentral/fileexchange/1039-hline-and-vlinehttp://www.mathworks.com/matlabcentral/fileexchange/1039-hline-and-vlinehttp://www.mathworks.com/matlabcentral/fileexchange/1039-hline-and-vlinehttp://www.mathworks.nl/matlabcentral/fileexchange/8430-flow-cytometry-data-reader-and-visualization/content/html/facsdemo.htmlhttp://www.mathworks.nl/matlabcentral/fileexchange/8430-flow-cytometry-data-reader-and-visualization/content/html/facsdemo.htmlhttp://www.mathworks.com/matlabcentral/fileexchange/1039-hline-and-vline

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Published with MATLAB 8.0