diff --git a/03_flow_MEFL/exercises.m b/03_flow_MEFL/exercises.m index 5022217..28ca211 100644 --- a/03_flow_MEFL/exercises.m +++ b/03_flow_MEFL/exercises.m @@ -71,8 +71,7 @@ CM = ColorModel(beadfile, blankfile, channels, colorfiles, colorpairfiles); CM = set_ERF_channel_name(CM, 'FITC-A'); % Name the channel we'll use for ERF units CM=set_dequantization(CM, 1); % important at low levels -CM=set_bead_plot(CM, 2); % 2 = show beads for all channels, even though only FITC will be used -CM=set_bead_min(CM, 1); % Don't consider beads less than this amount +TASBEConfig.set('beads.rangeMin', 1); % Don't consider beads less than this (log10) amount % Things we'll talk about in the next section... CM=set_translation_plot(CM, true); CM=set_translation_channel_min(CM,[2,2,2]); @@ -88,15 +87,15 @@ % The FITC channel is the one that we will key off % The identification is pretty terrible, though! % Two things are going wrong here: -% 1) We're getting smearing of peaks from autofluorescence: bead_min should be raised +% 1) We're getting smearing of peaks from autofluorescence: beads.rangeMin should be raised % 2) Automatic threshold detection is not finding the right value, because there % is not a distinct enough "valley" in the FITC graph % Notice also that you got a warning that: "Warning: Bead calibration probably incorrect" % When peaks are mis-detected, this typically leads to a bad fit against the % expected sequence gaps, giving warning of failures. -CM=set_bead_min(CM, 2); % Don't consider beads less than this amount -CM=set_bead_peak_threshold(CM, 200); % override default peak threshold +TASBEConfig.set('beads.rangeMin', 2); % Don't consider beads less than this (log10) amount +TASBEConfig.set('beads.peakThreshold', 200); % override default peak threshold CM = resolve(CM); % We get a new warning: "Warning: Only one bead peak found, assuming brightest" diff --git a/template_analysis/LacI-CAGop_histogramFile.csv b/template_analysis/LacI-CAGop_histogramFile.csv new file mode 100644 index 0000000..0602c1e --- /dev/null +++ b/template_analysis/LacI-CAGop_histogramFile.csv @@ -0,0 +1,841 @@ +ID,BinCenters,BinCount_FITC_A,BinCount_PE_Tx_Red_YG_A,BinCount_Pacific_Blue_A +Dox 0.1,11220.1845430196,6799,2200,1383 +,14125.3754462276,8012,2732,2696 +,17782.7941003892,8780,3327,2638 +,22387.2113856834,8563,4637,2632 +,28183.8293126445,7622,4623,3741 +,35481.3389233575,6328,5595,4708 +,44668.3592150964,3929,5939,5301 +,56234.1325190349,1815,6289,5435 +,70794.5784384137,511,5738,5800 +,89125.0938133746,124,4272,4745 +,112201.845430196,20,3096,4170 +,141253.754462276,4,2285,3253 +,177827.941003892,4,2339,2923 +,223872.113856834,2,2546,3272 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+,22387211.3856834,43,17,1777 +,28183829.3126445,20,7,1490 +,35481338.9233575,7,6,1079 +,44668359.2150963,3,4,764 +,56234132.5190349,2,1,516 +,70794578.4384137,0,0,376 +,89125093.8133746,0,0,224 +,112201845.430197,0,0,143 +,141253754.462275,0,0,107 +,177827941.003892,0,0,57 +,223872113.856835,0,0,28 +,281838293.126445,0,0,19 +,354813389.233576,0,0,9 +,446683592.150962,0,0,2 +,562341325.190349,0,0,1 +,707945784.38414,0,0,0 +,891250938.133744,0,0,0 +,1122018454.30197,0,0,0 +,1412537544.62275,0,0,0 +,1778279410.03892,0,0,0 +,2238721138.56835,0,0,0 +,2818382931.26445,0,0,0 +,3548133892.33576,0,0,0 +,4466835921.50962,0,0,0 +,5623413251.90349,0,0,0 +,7079457843.8414,0,0,0 +,8912509381.33744,0,0,0 diff --git a/template_analysis/LacI-CAGop_statisticsFile.csv b/template_analysis/LacI-CAGop_statisticsFile.csv new file mode 100644 index 0000000..3b50b82 --- /dev/null +++ b/template_analysis/LacI-CAGop_statisticsFile.csv @@ -0,0 +1,15 @@ +ID,BinCount_FITC_A,BinCount_PE_Tx_Red_YG_A,BinCount_Pacific_Blue_A,GeoMean_FITC_A,GeoMean_PE_Tx_Red_YG_A,GeoMean_Pacific_Blue_A,GeoStdDev_FITC_A,GeoStdDev_PE_Tx_Red_YG_A,GeoStdDev_Pacific_Blue_A +Dox 0.1,52519,109304,119534,22165.025452981,249480.031428636,410631.479202476,1.60060851602962,6.76534630618315,8.10003529761778 +Dox 0.2,42805,88422,95699,22188.0743351113,248909.635637894,407573.027865249,1.5989574034829,6.86705919259453,8.13062195345944 +Dox 0.5,40922,85388,93073,22108.805065838,257671.246116955,426008.54075171,1.59814139083964,6.86483601671476,8.12292552499894 +Dox 1.0,35873,75011,81845,22047.9528459911,258753.029631657,433436.305211408,1.60355897065308,6.91542171813179,8.21351966835268 +Dox 2.0,40117,83646,91874,22156.9833530256,250988.198177039,430944.214811771,1.60347980970474,6.75640141682951,8.10705860949241 +Dox 5.0,47388,97825,108168,22546.8133305892,248623.129202773,427654.749184805,1.64272376558834,6.80195719151201,8.27411543382126 +Dox 10.0,44944,91893,100527,22812.2405422446,254573.233427275,425856.502036798,1.70295768283413,6.76177886966528,8.12197873781665 +Dox 20.0,49108,95512,104801,25391.5763608897,257381.737571485,440725.312703547,1.99137655091,6.77005600726259,8.29382800299649 +Dox 50.0,45594,75243,82319,37910.9571859584,242175.06260393,462127.788442408,3.05675286196286,6.45792828797547,8.40520472709297 +Dox 100.0,52306,79583,88127,48912.9408807794,232673.026366744,472205.546041661,3.68677556998661,6.17018059244424,8.41844135833363 +Dox 200.0,64184,86943,96283,69242.0431237276,210677.034934462,465926.99712996,4.50684333785668,5.86855444787047,8.23925696594572 +Dox 500.0,80309,94076,108022,109305.024898359,175132.19946249,567293.173746977,5.28188595606136,5.27799922540984,8.7369227720754 +Dox 1000.0,92312,95920,113067,159093.739305107,154512.535696275,671434.882968259,5.60188995678396,4.70610037710353,8.58928321844016 +Dox 2000.0,102411,99664,119397,194717.045060966,141752.63631461,746082.759983345,5.57735408403808,4.38999273430913,8.43911397110291 diff --git a/template_analysis/batch_template.m b/template_analysis/batch_template.m index 7303e25..7e95e08 100644 --- a/template_analysis/batch_template.m +++ b/template_analysis/batch_template.m @@ -1,5 +1,6 @@ % This template shows how to perform a simple batch analysis of a set of conditions % Each color is analyzed independently +TASBEConfig.checkpoint('init'); % load the color model load('../template_colormodel/CM120312.mat'); @@ -48,24 +49,10 @@ [results sampleresults] = per_color_constitutive_analysis(CM,file_pairs,{'EBFP2','EYFP','mKate'},AP); % Make output plots -TASBEConfig.set('OS.StemName','LacI-CAGop'); -TASBEConfig.set('OS.FixedInputAxis',[1e4 1e10]); +TASBEConfig.set('OutputSettings.StemName','LacI-CAGop'); +TASBEConfig.set('OutputSettings.FixedInputAxis',[1e4 1e10]); plot_batch_histograms(results,sampleresults,{'b','y','r'},CM); -[statisticsFile, histogramFile] = serializeBatchOutput(file_pairs, CM, AP, sampleresults, '../'); +[statisticsFile, histogramFile] = serializeBatchOutput(file_pairs, CM, AP, sampleresults); save('LacI-CAGop-batch.mat','AP','bins','file_pairs','results','sampleresults'); - -% Dump CSV files: -fprintf('Dumping CSV files\n'); -fid = fopen('LacI-CAGop-batch.csv','w'); -fprintf(fid,'Device ID,datapoints,,,log10 Mean,,,Std.Dev. of mean (fold)\n'); -fprintf(fid,',EBFP2,EYFP,mKate,EBFP2,EYFP,mKate,EBFP2,EYFP,mKate\n'); -for i=1:n_conditions - fprintf(fid,'%s,',file_pairs{i,1}); - fprintf(fid,'%d,',sum(results{i}.bincounts)); - fprintf(fid,'%d,',log10(results{i}.means)); - fprintf(fid,'%d,',results{i}.stdofmeans); - fprintf(fid,'\n'); -end -fclose(fid); diff --git a/template_analysis/plusminus_template.m b/template_analysis/plusminus_template.m index bc87c08..9dfd8e3 100755 --- a/template_analysis/plusminus_template.m +++ b/template_analysis/plusminus_template.m @@ -1,4 +1,5 @@ % This file shows how to perform a batch of +/- comparisons +TASBEConfig.checkpoint('init'); % load the color model load('../template_colormodel/CM120312.mat'); @@ -46,15 +47,14 @@ }; % Execute the actual analysis -TASBEConfig.set('OS.DeviceName',device_name); +TASBEConfig.set('OutputSettings.DeviceName',device_name); results = process_plusminus_batch( CM, batch_description, AP); % Make additional output plots for i=1:numel(results) - TASBEConfig.set('OS.StemName',batch_description{i}{1}); - TASBEConfig.set('OS.DeviceName',device_name); - TASBEConfig.set('OS.Directory','plots/'); - TASBEConfig.set('OS.PlotTickMarks',1); + TASBEConfig.set('OutputSettings.StemName',batch_description{i}{1}); + TASBEConfig.set('OutputSettings.DeviceName',device_name); + TASBEConfig.set('OutputSettings.PlotTickMarks',1); plot_plusminus_comparison(results{i}) end diff --git a/template_analysis/transfercurve_template.m b/template_analysis/transfercurve_template.m index 50cb574..40105c3 100644 --- a/template_analysis/transfercurve_template.m +++ b/template_analysis/transfercurve_template.m @@ -1,5 +1,6 @@ % This template shows how to perform parametric analysis of a transient % transfection transfer curve +TASBEConfig.checkpoint('init'); % load the color model load('../template_colormodel/CM120312.mat'); @@ -55,18 +56,18 @@ results = summarize_data(CM,experiment,AP,sampleresults); % Make output plots -TASBEConfig.set('OS.StemName','Fine'); +TASBEConfig.set('OutputSettings.StemName','Fine'); % Plot how the constitutive fluorescence was distributed -TASBEConfig.set('OS.DeviceName',device_name); +TASBEConfig.set('OutputSettings.DeviceName',device_name); plot_bin_statistics(sampleresults); % Plot the relation between inducer and input fluorescence -TASBEConfig.set('OS.DeviceName',inducer_name); +TASBEConfig.set('OutputSettings.DeviceName',inducer_name); plot_inducer_characterization(results); % Plot the relation between input and output fluorescence -TASBEConfig.set('OS.DeviceName',device_name); +TASBEConfig.set('OutputSettings.DeviceName',device_name); plot_IO_characterization(results); % Save the results of computation diff --git a/template_colormodel/CM120312.mat b/template_colormodel/CM120312.mat index 38d0a35..4d166da 100644 Binary files a/template_colormodel/CM120312.mat and b/template_colormodel/CM120312.mat differ diff --git a/template_colormodel/make_color_model.m b/template_colormodel/make_color_model.m index f6d5b7c..cdedcd3 100644 --- a/template_colormodel/make_color_model.m +++ b/template_colormodel/make_color_model.m @@ -1,4 +1,4 @@ -% auto generated by colorModel.py, modified by us +TASBEConfig.checkpoint('init'); stem0312 = '../example_controls/2012-03-12_'; @@ -47,27 +47,26 @@ colorpairfiles{2} = {channels{1}, channels{3}, channels{2}, [stem0312 'mkate_EBFP2_EYFP_P3.fcs']}; CM = ColorModel(beadfile, blankfile, channels, colorfiles, colorpairfiles); -CM=set_bead_plot(CM, 2); % 2 = detailed plots; 1 = minimal plot; 0 = no plot CM=set_translation_plot(CM, true); CM=set_noise_plot(CM, true); -CM=set_bead_model(CM,'SpheroTech RCP-30-5A'); % Entry from BeadCatalog.xls matching your beads -CM=set_bead_batch(CM,'Lot AA01, AA02, AA03, AA04, AB01, AB02, AC01, GAA01-R'); % Entry from BeadCatalog.xls containing your lot -% Can also set bead channel if, for some reason, you don't want to use fluorescein as standard +TASBEConfig.set('beads.beadModel','SpheroTech RCP-30-5A'); % Entry from BeadCatalog.xls matching your beads +TASBEConfig.set('beads.beadBatch','Lot AA01, AA02, AA03, AA04, AB01, AB02, AC01, GAA01-R'); % Entry from BeadCatalog.xls containing your lot +% Can also set bead channel if, for some reason, you don't want to use fluorescein as standard % This defaults to FITC as it is strongly recommended to use fluorescein standards. -% CM=set_bead_channel(CM,'FITC'); +% TASBEConfig.set('beadChannel','FITC'); -% Ignore all bead data below 10^[bead_min] as being too "smeared" with noise -CM=set_bead_min(CM, 2); +% Ignore all bead data below 10^[rangeMin] as being too "smeared" with noise +TASBEConfig.set('beads.rangeMin', 2); % The peak threshold determines the minumum count per bin for something to % be considered part of a peak. Set if automated threshold finds too many or few peaks -%CM=set_bead_peak_threshold(CM, 200); +%TASBEConfig.set('beads.peakThreshold', 200); CM=set_ERF_channel_name(CM, 'FITC-A'); % Ignore channel data for ith channel if below 10^[value(i)] CM=set_translation_channel_min(CM,[2,2,2]); % When dealing with very strong fluorescence, use secondary channel to segment -%settings = setSetting(settings,'SecondaryBeadChannel','PE-Texas_Red-A'); +% TASBEConfig.set('beads.secondaryBeadChannel','PE-Tx-Red-YG-A'); CM = add_filter(CM,autogate); % Execute and save the model