Merge pull request #20 from TASBE/tutorial.ltiberio.bug86

Tutorial.ltiberio.bug86

Author: jakebeal

template_analysis/batch_template.m

@@ -19,6 +19,9 @@
 AP=setPemDropThreshold(AP,5');
 % Add autofluorescence back in after removing for compensation?
 AP=setUseAutoFluorescence(AP,false');
+% By default, analysis tries to fit constitutive to transformed and non-transformed components
+% If your distribution is more complex or less complex, you can change the number of components
+% AP=setNumGaussianComponents(AP,3);
 
 % Make a map of condition names to file sets
 stem1011 = '../example_assay/LacI-CAGop_';
@@ -47,7 +50,7 @@
 % Make output plots
 OS = OutputSettings('LacI-CAGop','','','plots');
 OS.FixedInputAxis = [1e4 1e10];
-plot_batch_histograms(results,sampleresults,OS,{'b','y','r'});
+plot_batch_histograms(results,sampleresults,OS,{'b','y','r'},CM);
 
 save('LacI-CAGop-batch.mat','AP','bins','file_pairs','OS','results','sampleresults');
 

template_analysis/plots/placeholder.txt

@@ -23,6 +23,9 @@
 AP=setPemDropThreshold(AP,5');
 % Add autofluorescence back in after removing for compensation?
 AP=setUseAutoFluorescence(AP,false');
+% By default, analysis tries to fit constitutive to “transformed” and “non-transformed” components
+% If your distribution is more complex or less complex, you can change the number of components
+% AP=setNumGaussianComponents(AP,3);
 
 % Make a map of the batches of plus/minus comparisons to test
 % This analysis supports two variables: a +/- variable and a "tuning" variable

template_analysis/plusminus_template.m

@@ -25,6 +25,9 @@
 AP=setPemDropThreshold(AP,5');
 % Add autofluorescence back in after removing for compensation?
 AP=setUseAutoFluorescence(AP,false');
+% By default, analysis tries to fit constitutive to “transformed” and “non-transformed” components
+% If your distribution is more complex or less complex, you can change the number of components
+% AP=setNumGaussianComponents(AP,3);
 
 % Make a map of induction levels to file sets
 stem1011 = '../example_assay/LacI-CAGop_';

template_analysis/transfercurve_template.m

@@ -25,7 +25,7 @@
 channels{1} = Channel('FITC-A', 488, 515, 20);
 channels{1} = setPrintName(channels{1}, 'EYFP'); % Name to print on charts
 channels{1} = setLineSpec(channels{1}, 'y'); % Color for lines, when needed
-colorfiles{1} = [stem0312 'EYFP_P3.fcs'];
+colorfiles{1} = [stem0312 'EYFP_P3.fcs']; % If there is only one channel, the color file is optional
 
 channels{2} = Channel('PE-Tx-Red-YG-A', 561, 610, 20);
 channels{2} = setPrintName(channels{2}, 'mKate');