Merge pull request #38 from TASBE/coverney.excel

 Renamed example_assay files

Author: jakebeal

01_flow_cytometry/exercises.m

@@ -15,10 +15,10 @@
 % Examples of flow data (Fig1 to Fig4)
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % pure scatter - often hard to interpret
-fcs_scatter([dosedata 'LacI-CAGop_C4_C04_P3.fcs'],'PE-Tx-Red-YG-A','Pacific Blue-A',0,[0 0; 6 6],1); % Fig1
+fcs_scatter([dosedata 'LacI-CAGop_C4_P3.fcs'],'PE-Tx-Red-YG-A','Pacific Blue-A',0,[0 0; 6 6],1); % Fig1
 fcs_scatter([colordata '07-29-11_EYFP_P3.fcs'],'FITC-A','Pacific Blue-A',0,[0 0; 6 6],1); % Fig2
 % smoothed density plot omits details but often summarizes collective better
-data1 = fcs_scatter([dosedata 'LacI-CAGop_C4_C04_P3.fcs'],'PE-Tx-Red-YG-A','Pacific Blue-A',1,[0 0; 6 6],1); % Fig3
+data1 = fcs_scatter([dosedata 'LacI-CAGop_C4_P3.fcs'],'PE-Tx-Red-YG-A','Pacific Blue-A',1,[0 0; 6 6],1); % Fig3
 data2 = fcs_scatter([colordata '07-29-11_EYFP_P3.fcs'],'FITC-A','Pacific Blue-A',1,[0 0; 6 6],1); % Fig4
 
 % Things to notice:
@@ -82,7 +82,7 @@
 filtered = read_filtered_au(CM,[colordata '07-29-11_EYFP_P3.fcs']); % applies any filters set in ColorModel
 
 CM = set_dequantization(CM,true); % dequantization adds noise to spread the data out more, especially useful at low levels
-[dequantized hdr] = read_filtered_au(CM,[dosedata 'LacI-CAGop_C4_C04_P3.fcs']);
+[dequantized hdr] = read_filtered_au(CM,[dosedata 'LacI-CAGop_C4_P3.fcs']);
 xc = dequantized(:,10); yc = dequantized(:,11);
 pos = xc>0 & yc>0;
 figure; smoothhist2D(log10([xc(pos) yc(pos)]),10,[200, 200],[],'image',[0 0; 6 6]); % Fig5

02_flow_compensation/exercises.m

@@ -114,8 +114,8 @@
 CM = set_ERF_channel_name(CM, 'FITC-A'); % We'll explain this in the next exercise
 
 % Now let's read some files...
-raw = read_filtered_au(CM,[dosedata 'LacI-CAGop_C3_C03_P3.fcs']);
-compensated = readfcs_compensated_au(CM,[dosedata 'LacI-CAGop_C3_C03_P3.fcs'],0,1);
+raw = read_filtered_au(CM,[dosedata 'LacI-CAGop_C3_P3.fcs']);
+compensated = readfcs_compensated_au(CM,[dosedata 'LacI-CAGop_C3_P3.fcs'],0,1);
 % You should see an error: need to "resolve" the color model first! Comment
 % out above line of code and run again.
 
@@ -159,7 +159,7 @@
 % even when it can be compensated for.
 
 
-compensated = readfcs_compensated_au(CM,[dosedata 'LacI-CAGop_C3_C03_P3.fcs'],0,1);
+compensated = readfcs_compensated_au(CM,[dosedata 'LacI-CAGop_C3_P3.fcs'],0,1);
 % The last two arguments are:
 % 1) Whether to add autofluorescence back in after reading (generally not done)
 % 2) Whether to map all values <= 0 to 1 (which is zero on the log scale)