change FITC, MEFL to ERF where appropriate

02_flow_compensation/exercises.m

@@ -103,7 +103,7 @@
 
 colorpairfiles = {};
 CM = ColorModel(beadfile, blankfile, channels, colorfiles, colorpairfiles);
-CM = set_FITC_channel_name(CM, 'FITC-A'); % We'll explain this in the next exercise
+CM = set_ERF_channel_name(CM, 'FITC-A'); % We'll explain this in the next exercise
 settings = TASBESettings();
 
 % Now let's read some files...
@@ -114,7 +114,7 @@
 CM = resolve(CM,settings);
 
 % Ignore the warnings about finding only one bead peak and translation and 
-% mapping files: those have to do with MEFL conversion, which we'll cover
+% mapping files: those have to do with ERF conversion, which we'll cover
 % in our next exercise
 
 % Resolving the colormodel just produced a whol lot of files: let's take a

03_flow_MEFL/exercises.m

@@ -39,9 +39,10 @@
 
 % Each channel is calibrated to a separate standard fluorophore.  The units
 % are ME[F]: Mean Equivalent [Fluorophore abbreviation].
-% They are also generically called MESF (Mean Equivalent Standard Fluorophore), 
+% They are also generically called ERF (Equivalent Reference Fluorophore), 
+% or MESF (Mean Equivalent Standard Fluorophore)
 % which is problematic because it makes different units appear the same.
-% We standardize on one: MEFL, from the FITC channel
+% We recommend standardizing on one: MEFL, from the FITC channel
 
 % So, beads give us the ability to standardize any channel, but no converstion
 % between the units of channels.  That is what we do with multi-color controls (next section)
@@ -69,7 +70,7 @@
 
 CM = ColorModel(beadfile, blankfile, channels, colorfiles, colorpairfiles);
 settings = TASBESettings();
-CM = set_FITC_channel_name(CM, 'FITC-A'); % Name the channel we'll use for MEFL units
+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
@@ -124,7 +125,7 @@
 % Translation between channels:
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
-% How do we measure red or blue in MEFL?
+% How do we measure red or blue in ERF?
 % Note that the different channels have wildly different calibrations!
 % We need a conversion factor on our fluorophores, to answer questions
 % of the form: "what if I had used yellow here instead of red?"

template_analysis/LacI-CAGop-batch.csv

@@ -1,16 +1,16 @@
 Device ID,datapoints,,,log10 Mean,,,Std.Dev. of mean (fold)
 ,EBFP2,EYFP,mKate,EBFP2,EYFP,mKate,EBFP2,EYFP,mKate
-Dox 0.1,18071,38789,42669,4.331844e+00,5.329899e+00,5.569393e+00,1,1,1,
-Dox 0.2,15306,32317,35251,4.330452e+00,5.333015e+00,5.566198e+00,1,1,1,
-Dox 0.5,14115,30495,33528,4.326479e+00,5.337378e+00,5.584684e+00,1,1,1,
-Dox 1.0,12387,26456,29089,4.326265e+00,5.323159e+00,5.573961e+00,1,1,1,
-Dox 2.0,14199,30747,34066,4.326872e+00,5.324492e+00,5.588860e+00,1,1,1,
-Dox 5.0,17622,37529,41776,4.333674e+00,5.323194e+00,5.577985e+00,1,1,1,
-Dox 10.0,16523,35248,38757,4.332921e+00,5.341809e+00,5.592516e+00,1,1,1,
-Dox 20.0,17540,35878,39649,4.360046e+00,5.337268e+00,5.600788e+00,1,1,1,
-Dox 50.0,16185,28125,30951,4.510488e+00,5.311045e+00,5.604541e+00,1,1,1,
-Dox 100.0,18393,29060,32566,4.636256e+00,5.308469e+00,5.633793e+00,1,1,1,
-Dox 200.0,21755,30378,34239,4.775760e+00,5.261884e+00,5.616150e+00,1,1,1,
-Dox 500.0,27885,33234,38616,4.979428e+00,5.192667e+00,5.706803e+00,1,1,1,
-Dox 1000.0,30671,32264,38350,5.147594e+00,5.153512e+00,5.785773e+00,1,1,1,
-Dox 2000.0,34897,34188,41553,5.234729e+00,5.115233e+00,5.836853e+00,1,1,1,
+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,
+Dox 0.5,40799,85195,92821,4.342561e+00,5.406055e+00,5.622935e+00,1,1,1,
+Dox 1.0,35745,74814,81622,4.340866e+00,5.406947e+00,5.630341e+00,1,1,1,
+Dox 2.0,39959,83476,91641,4.342808e+00,5.395057e+00,5.628313e+00,1,1,1,
+Dox 5.0,47149,97621,108001,4.348411e+00,5.390884e+00,5.627314e+00,1,1,1,
+Dox 10.0,44674,91712,100259,4.351312e+00,5.401429e+00,5.622702e+00,1,1,1,
+Dox 20.0,48738,95318,104607,4.393307e+00,5.406043e+00,5.639542e+00,1,1,1,
+Dox 50.0,45415,75068,82129,4.570854e+00,5.379279e+00,5.659200e+00,1,1,1,
+Dox 100.0,52009,79365,87965,4.677907e+00,5.361092e+00,5.669696e+00,1,1,1,
+Dox 200.0,63959,86725,96095,4.832942e+00,5.318321e+00,5.663546e+00,1,1,1,
+Dox 500.0,80055,93869,107840,5.031924e+00,5.238768e+00,5.749740e+00,1,1,1,
+Dox 1000.0,92173,95703,112858,5.198495e+00,5.184191e+00,5.822585e+00,1,1,1,
+Dox 2000.0,102262,99465,119276,5.286472e+00,5.147556e+00,5.870413e+00,1,1,1,

template_analysis/batch_template.m

@@ -8,7 +8,7 @@
 experimentName = 'LacI Transfer Curve';
 
 % Configure the analysis
-% Analyze on a histogram of 10^[first] to 10^[third] MEFL, with bins every 10^[second]
+% Analyze on a histogram of 10^[first] to 10^[third] ERF, with bins every 10^[second]
 bins = BinSequence(4,0.1,10,'log_bins');
 
 % Designate which channels have which roles

template_analysis/plusminus_template.m

@@ -9,7 +9,7 @@
 inducer_name = '100xDox';
 
 % Configure the analysis
-% Analyze on a histogram of 10^[first] to 10^[third] MEFL, with bins every 10^[second]
+% Analyze on a histogram of 10^[first] to 10^[third] ERF, with bins every 10^[second]
 bins = BinSequence(4,0.1,10,'log_bins');
 
 % Designate which channels have which roles

template_analysis/transfercurve_template.m

@@ -11,7 +11,7 @@
 inducer_name = 'Dox';
 
 % Configure the analysis
-% Analyze on a histogram of 10^[first] to 10^[third] MEFL, with bins every 10^[second]
+% Analyze on a histogram of 10^[first] to 10^[third] ERF, with bins every 10^[second]
 bins = BinSequence(4,0.1,10,'log_bins');
 
 % Designate which channels have which roles

template_colormodel/make_color_model.m

@@ -37,8 +37,8 @@
 channels{3} = setLineSpec(channels{3}, 'b');
 colorfiles{3} = [stem0312 'ebfp2_P3.fcs'];
 
-% Multi-color controls are used for converting other colors into MEFL units
-% Any channel without a control mapping it to MEFL will be left in arbirary units.
+% Multi-color controls are used for converting other colors into ERF units
+% Any channel without a control mapping it to ERF will be left in arbirary units.
 colorpairfiles = {};
 % Entries are: channel1, channel2, constitutive channel, filename
 % This allows channel1 and channel2 to be converted into one another.
@@ -60,7 +60,7 @@
 % 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);
-CM=set_FITC_channel_name(CM, 'FITC-A');
+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]);