diff --git a/template_analysis/LacI-CAGop-batch.csv b/template_analysis/LacI-CAGop-batch.csv index 8b44199..d8f8572 100644 --- a/template_analysis/LacI-CAGop-batch.csv +++ b/template_analysis/LacI-CAGop-batch.csv @@ -1,4 +1,4 @@ -Device ID,datapoints,,,log10 Mean,,,Std.Dev. of mean (fold) +Device Id,datapoints,,,log10 Mean,,,Std.Dev. of mean (fold) ,EBFP2,EYFP,mKate,EBFP2,EYFP,mKate,EBFP2,EYFP,mKate Dox 0.1,52482,109175,119351,4.345084e+00,5.394359e+00,5.609663e+00,1,1,1, Dox 0.2,42682,88230,95559,4.344227e+00,5.391166e+00,5.606492e+00,1,1,1, diff --git a/template_analysis/LacI-CAGop-batch.mat b/template_analysis/LacI-CAGop-batch.mat index be050a2..e14a3bb 100644 Binary files a/template_analysis/LacI-CAGop-batch.mat and b/template_analysis/LacI-CAGop-batch.mat differ diff --git a/template_analysis/LacI-CAGop_histogramFile.csv b/template_analysis/LacI-CAGop_histogramFile.csv index 0602c1e..9196487 100644 --- a/template_analysis/LacI-CAGop_histogramFile.csv +++ b/template_analysis/LacI-CAGop_histogramFile.csv @@ -1,49 +1,49 @@ -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 -,281838.293126445,2,2845,3603 -,354813.389233575,1,3389,4013 -,446683.592150963,2,3757,4009 -,562341.325190349,1,4030,3976 -,707945.784384137,0,4246,4139 -,891250.938133746,0,4436,4189 -,1122018.45430196,0,4502,4183 -,1412537.54462276,0,4289,4099 -,1778279.41003892,0,4007,3881 -,2238721.13856834,0,3630,3826 -,2818382.93126445,0,3244,3684 -,3548133.89233575,0,2738,3506 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+,11220184.5430196,224,130,2646 +,14125375.4462275,111,91,2333 +,17782794.1003892,66,52,1856 +,22387211.3856834,42,34,1559 +,28183829.3126445,13,19,1240 +,35481338.9233575,9,11,926 +,44668359.2150963,6,6,761 +,56234132.5190349,0,3,486 +,70794578.4384137,1,1,344 +,89125093.8133746,0,1,248 +,112201845.430197,0,0,164 +,141253754.462275,0,0,87 +,177827941.003892,0,0,66 +,223872113.856835,0,0,42 +,281838293.126445,0,0,12 ,354813389.233576,0,0,2 ,446683592.150962,0,0,0 ,562341325.190349,0,0,0 @@ -779,51 +779,51 @@ Dox 1000.0,11220.1845430196,3427,2030,1001 ,5623413251.90349,0,0,0 ,7079457843.8414,0,0,0 ,8912509381.33744,0,0,0 -Dox 2000.0,11220.1845430196,3160,2135,887 -,14125.3754462276,3941,2505,1691 -,17782.7941003892,4594,3214,1600 -,22387.2113856834,4704,4285,1767 -,28183.8293126445,4761,4560,2539 -,35481.3389233575,4844,5420,3175 -,44668.3592150964,3991,6148,3640 -,56234.1325190349,3111,6736,3920 -,70794.5784384137,2778,6376,4263 -,89125.0938133746,2770,5499,3788 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+,89125.0938133746,2743,5504,3724 +,112201.845430196,2950,4726,3458 +,141253.754462276,3241,4165,3201 +,177827.941003892,3816,4164,2731 +,223872.113856834,4190,4160,2927 +,281838.293126445,4731,4333,3206 +,354813.389233575,4950,4426,3604 +,446683.592150963,5329,4312,3854 +,562341.325190349,5215,4282,3953 +,707945.784384137,5127,3868,4355 +,891250.938133746,4621,3343,4340 +,1122018.45430196,4323,2856,4472 +,1412537.54462276,3776,2144,4428 +,1778279.41003892,2981,1769,4663 +,2238721.13856834,2420,1330,4604 +,2818382.93126445,1774,935,4566 +,3548133.89233575,1347,640,4367 +,4466835.92150963,1028,475,4138 +,5623413.25190349,681,340,3914 +,7079457.84384139,527,217,3750 +,8912509.38133746,318,119,3304 ,11220184.5430196,208,88,3050 -,14125375.4462275,113,47,2518 -,17782794.1003892,71,26,2170 -,22387211.3856834,43,17,1777 -,28183829.3126445,20,7,1490 -,35481338.9233575,7,6,1079 +,14125375.4462275,112,47,2539 +,17782794.1003892,73,26,2178 +,22387211.3856834,43,17,1768 +,28183829.3126445,20,7,1518 +,35481338.9233575,7,7,1086 ,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 +,56234132.5190349,2,1,521 +,70794578.4384137,0,0,381 +,89125093.8133746,0,0,225 +,112201845.430197,0,0,147 +,141253754.462275,0,0,106 +,177827941.003892,0,0,58 ,223872113.856835,0,0,28 -,281838293.126445,0,0,19 +,281838293.126445,0,0,20 ,354813389.233576,0,0,9 ,446683592.150962,0,0,2 ,562341325.190349,0,0,1 diff --git a/template_analysis/LacI-CAGop_statisticsFile.csv b/template_analysis/LacI-CAGop_statisticsFile.csv index 3b50b82..5360a65 100644 --- a/template_analysis/LacI-CAGop_statisticsFile.csv +++ b/template_analysis/LacI-CAGop_statisticsFile.csv @@ -1,15 +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 +Id,BinCount_EYFP_MEFL,BinCount_mKate_MEFL,BinCount_EBFP2_MEFL,GeoMean_EYFP_MEFL,GeoMean_mKate_MEFL,GeoMean_EBFP2_MEFL,GeoStdDev_EYFP_MEFL,GeoStdDev_mKate_MEFL,GeoStdDev_EBFP2_MEFL +Dox 0.1,52543,109303,119534,22166.3892127889,249505.506639999,411999.810945553,1.60084886418747,6.76458209037627,8.11197502902936 +Dox 0.2,42961,88780,96134,22197.3585165184,248829.70817965,409394.898134347,1.5995070299618,6.86183513588093,8.13315768191834 +Dox 0.5,41068,85629,93335,22115.1197730026,257612.933359406,427307.331165168,1.59855221637465,6.86703936713332,8.13649642809853 +Dox 1.0,35885,75014,81850,22051.6025368397,258759.473832509,434883.202135694,1.60343323201745,6.91515508495032,8.22562195437244 +Dox 2.0,40232,83870,92116,22157.0039944486,250987.355176404,432747.679233904,1.60382703945833,6.75567397806102,8.1161867549061 +Dox 5.0,47577,98169,108567,22546.6135362971,248794.832186403,429718.109247681,1.64276006827997,6.8028174325622,8.28125154154586 +Dox 10.0,45162,92315,101005,22816.101591211,254771.721342507,427711.99314504,1.70266995382062,6.75700767951142,8.1256863136358 +Dox 20.0,49316,95836,105151,25395.162349766,257224.545603477,442090.53529095,1.99180114843258,6.76888717898788,8.30694414618095 +Dox 50.0,45606,75244,82319,37917.3791053317,242181.479602933,463724.365537185,3.0573604948584,6.45752985767407,8.41842393115125 +Dox 100.0,52347,79642,88193,48930.3361458285,232755.190533719,474127.864142354,3.68843886902498,6.16925999118782,8.43004507832824 +Dox 200.0,64190,86947,96290,69261.8115521469,210676.507867137,467542.79950384,4.50779976930361,5.86799325713468,8.25341761300255 +Dox 500.0,80463,94229,108153,109356.802892914,175204.602854373,570194.401672882,5.2828897137624,5.27822277454789,8.75049608606087 +Dox 1000.0,92324,95925,113074,159145.647766921,154514.40938562,673960.347664984,5.60321229394227,4.70603829679273,8.59943577186356 +Dox 2000.0,102447,99697,119441,194826.405465652,141750.506571001,749269.588700572,5.57840977677493,4.39004014516118,8.44799549981408 diff --git a/template_analysis/batch_template.m b/template_analysis/batch_template.m index 7e95e08..3ea3d32 100644 --- a/template_analysis/batch_template.m +++ b/template_analysis/batch_template.m @@ -4,6 +4,9 @@ % load the color model load('../template_colormodel/CM120312.mat'); +% can also add filters, such as gating out all "low transfection" red less than 10^6 MEFL: +%CM = add_postfilter(CM,RangeFilter('PE-Tx-Red-YG-A',[1e6 inf])); + % set up metadata experimentName = 'LacI Transfer Curve'; diff --git a/template_colormodel/CM120312.mat b/template_colormodel/CM120312.mat index 4d166da..81fe5cf 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 cdedcd3..208b1b2 100644 --- a/template_colormodel/make_color_model.m +++ b/template_colormodel/make_color_model.m @@ -67,7 +67,7 @@ % When dealing with very strong fluorescence, use secondary channel to segment % TASBEConfig.set('beads.secondaryBeadChannel','PE-Tx-Red-YG-A'); -CM = add_filter(CM,autogate); +CM = add_prefilter(CM,autogate); % Execute and save the model CM=resolve(CM);