Compensation: Basic Principles
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1 Compensation: Basic Principles Bonus topic: Daytime Stargazing Mario Roederer ImmunoTechnology Section Vaccine Research Center, NIAID, NIH
2 Spectral Spillover Necessitates Compensation FITC PE Argon Laser FL1 FL
3 Spectral Spillover Necessitates Compensation Total signal detected in FL1 FITC PE Unwanted signal detected in FL2 = roughly 15% Argon Laser FL1 FL True PE = Total FL2 15% FL1
4 Compensation Converts From Measurement to Expression Uncompensated Compensated PE - no stain FL2-15%FL1 PE - no stain FITC CD3 Measured Fluorescence FITC CD3 Calculated Expression
5 Compensation in Linear Domain Uncompensated Lines indicate cells that express equal amounts of an antigen Compensated
6 Compensation in Log Domain Uncompensated Compensated Lines indicate cells that express equal amounts of an antigen
7 Compensation is a Transformation Grid Lines Equal Measurement Equal Expression Bivariate Plots Histograms of each measurement
8 Compensation in 2 colors: Mostly aesthetic? Accurate identification and enumeration of subsets is still possible in two color experiments (but not visual estimation of expression levels ) 10 4 Uncompensated 10 4 Compensated CD CD3 CD3
9 Compensation with 3 colors Accurate separation of populations can require a curved, two-dimensional surface This gets worse with more colors...
10 Compensation: Not just aesthetic Accurate discrimination of subsets is possible with uncompensated data However, this is true only when the expression of all antigens is uniform on each subset (e.g., CD45 / CD3 / CD4 / CD8) Separation of populations may require multidimensional surfaces.
11 Compensation for more colors: It s not just pretty pictures Spillover from unviewed measurement channel can alter event positions without obvious visual evidence (no diagnostic diagonals!) Thus, gate positions may depend on unviewed measurement channels and be different for various tubes in a panel Gates could also be highly dependant on which subset is being analyzed!
12 Compensation in the Polychromatic World 10 4 Uncompensated Compensated? APC (Unstained) e Cy5.5APC CD
13 Compensation in the Polychromatic World But is it correctly compensated? Compensated?
14 Compensation in the Polychromatic World But is it correctly compensated? Compensated? No!
15 Compensation in the Polychromatic World But is it correctly compensated? Compensated? No!
16 Compensation in the Polychromatic World But is it correctly compensated? Compensated? No! Yes!
17 Compensation in the Polychromatic World But is it correctly compensated? Compensated? No! Yes!
18 Compensation in the Polychromatic World But is it correctly compensated? Compensated? No! Yes! We can t tell just by looking!
19 What s Missing From This Picture?
20 What s Missing From This Picture? Where are the stars?
21 Why can t we see stars during the day? On cloudless nights, we see lots of stars. On cloudless days, we rarely see stars. We call this the Blue Sky Effect. But.. Why? Nowhere on the web is this commonly-asked question answered correctly.
22 The Blue Sky Effect The stars are easily visible at night (well, in most places). When the sun rises the sky becomes blue and the stars are no longer detectable.
23 The Blue Sky Effect The stars are easily visible at night (well, in most places). When the sun rises the sky becomes blue and the stars are no longer detectable.
24 Why Doesn t it Look Like This? But light is additive. The white light from the stars should add to the blue scattered light from the sun why don t we see white pinpricks against the blue background?
25 Signal Quantification Intensity 100 0
26 How Bright Are the Stars? Intensity A star s intensity is the area under the histogram (i.e., counting the number of photons coming from the star).
27 How Bright Is The Sky? 1500 Intensity Y Intensity 100 0
28 Light Signals Are Additive 1500 Intensity
29 Star Light Brightness Is Unchanged Intensity Background-subtracted Intensity We determine the intensity of a star by subtracting the background. Here, the sky (background) is 1500 units, so subtract 1500 units from the measurements. A star s intensity is now the area under the histogram (# of photons only from the star)
30 But Measurements Are Not Perfect Every measurement we make has an error associated with it. The variance in a measurement is the distribution of values that you would get if you made the same measurement on exactly the same object time and again (and the object did not change over time). Variances can arise from a variety of sources: e.g., inherent variability, measurement error. The final variance is the sum of all of these. Measurement error can arise from many sources. When counting photons, for example, the minimum error is governed by Poisson statistics.
31 Measurement Errors Light intensity measurements are, essentially, photon counting. The minimum error will be ± n, where n = # of photons counted. Number of counts Error Precision 100 ±10 10% 10,000 ±100 1% 1,000,000 ±1, % As we increase the signal level, while the precision (CV) is getting better (smaller), the absolute error is increasing.
32 Measuring Sky Intensity 1500 Intensity
33 Star Light is Still Additive 1500 Intensity
34 Variation in Intensity Intensity
35 Variation in Intensity Intensity We estimate the intensity of a star by subtracting the background. Here, the sky (background) is, on average, 1500 units, so subtract 1500 units from the measurements.
36 Estimating Star Light Intensity 100 Intensity 0-100
37 Estimating Star Light Intensity 100 Intensity A star s intensity is, as before, the area under the histogram (# of photons only from the star)
38 Background Variance Ideal Measured Intensity Intensity
39 Background Variance Ideal Measured Intensity Intensity
40 Background Variance Is this negative light intensity? No. It is a negative estimated light intensity! And arbitrarily setting it to zero would introduce a systematic bias. Intensity
41 Why Can t We See Stars During the Day? Because the intensity of the star light is less than the variance of the intensity of the day light. Stars that are brighter than this variance can still be seen. The error on estimating the intensity of the star light will be at least as great as the variance of the day light... and can sometimes be <0.
42 Is This Related to Compensation? Completely Time since illumination Position in sky 29
43 Is This Related to Compensation? Completely. Compensation is the process by which we estimate a probe s contribution to a signal by subtracting estimated contributions from other sources. All the same principles apply: errors propagate; you cannot distinguish dim objects against high variance; you can get negative estimated signal intensities. 29
44 Imperfect Measurement Leads to Apparent Spread in Compensation 10 4 Uncompensated Compensated Spillover Fluorescence Primary Fluorescence (-200)
45 Imperfect Measurement Leads to Apparent Spread in Compensation 10 4 Uncompensated Compensated Spillover Fluorescence Primary Fluorescence Spreading manifests with a 1:2 Log:Log slope: square root relationship! Undercompensation manifests with a 1:1 Log:Log slope: linear relationship
46 The Actual Spread Background from PE-CD Lymphocytes <Cy7PE-A>: CD Variance contributed from background <PE-A>: CD8
47 Compensation Does NOT Introduce nor Increase Error: Compensation Only Reveals It! The measurement error is already present. Compensation does not increase this error, it does not change it, it does not introduce any more error. Compensation simply makes the error more apparent by shifting it to the low end of the logscale. Staining controls are necessary to define gate placement!
48 Staining Controls Staining controls are necessary to identify cells which do or do not express a given antigen. The threshold for positivity may depend on the amount of fluorescence in other channels!
49 FMO Controls FMO controls are a much better way to identify positive vs. negative cells FMO controls can also help identify problems in compensation that are not immediately visible FMO controls should be used whenever accurate discrimination is essential or when antigen expression is relatively low
50 Compensation Controls The purpose of a compensation control is to allow software to estimate how much spillover is happening. This needs to be as precise as possible! Precise and accurate compensation requires determining the slope as precisely as possible B560-A PE Cy7PE B710-A B530-A B530-A B530-A FITC FITC FITC Compensation = 7.4% = 0.56%
51 Compensation Controls The purpose of a compensation control is to allow software to estimate how much spillover is happening. This needs to be as precise as possible! Precise and accurate compensation requires determining the slope as precisely as possible. Small absolute errors can be large relative errors in compensation and dramatically impact data PE Cy7PE FITC FITC FITC Compensation = 0.56% Compensation = 0.86%
52 Compensation Controls There are only three rules to follow to ensure accurate compensation. All errors in compensation can be traced to a problem with one of these. 1. The experimental samples and control samples must be matched. Identical fluorochrome Identical instrument sensitivity (not settings) 2. The background (autofluorescence) for any given control s positive and negative events must be identical. 3. Each control s positive must be at least as bright as any experimental sample. To ensure precise compensation, collect enough events to precisely estimate median fluorescences in all channels: Beads: 5-10K Positive cells: 20-50K
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