Last updated: 2025-04-23

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Summary

Final cortisol value calculations were conducted using three methods:

  • Standard Method (Method A): Calculates cortisol concentration without correction for spiked samples.

  • Spike-Corrected Method (Method B): Adjusts for spiked samples to account for addition of a known amount of cortisol, following Nist et al. 2020.

  • Sam’s Method (Method C): Adjusts for spiked samples using a different equation

Results: As we see below, the formula used by Nist et al. results in negative values, which would mean that there is no cortisol in original samples. This could be an artifact of an extremely high absorbance level caused by an excessive amount of spike. Non-spiked samples, on the other hand, result in values that are within the range found in similar studies of cortisol in human hair.

Summary Nist et al. (A) Standard (B) Spike-Corrected (C) Sam’s
Mean cort conc (pg/mg) 16.376 -0.182 9.329
Median cort conc (pg/mg) 10.531 4.328 9.806
Range cort conc (pg/mg) 2.7 to 58.9 -29.933 to 11.763 2.716 to 22.002
Weight (mg) of my samples
Range 11 to 37.1
Mean 23.54
Median 22.4

Conclusions: After accounting for differences in dilution and weight, our results suggest future Assays should use the optimal parameters listed below:

  • Dilution of 250uL is preferable over 60uL
  • Non-spiked samples seem to generate expected results

Concerns

  • Spike results in unrealistic values
  • Could be explained by the higher weight of our samples
  • Dilution of 250uL results in values that are twice as big as with 60uL, but they should be very similar or at least overlap

Explanation of each variable used in calculations

  • Ave_Conc_pg/ml: average ELISA reading per sample in pg/mL

  • Weight_mg: hair weight in mg

  • Buffer_nl: assay buffer volume in nL → we convert to mL

  • Spike: binary indicator (1 = spiked sample)

  • SpikeVol_uL: volume of spike added in µL

  • Dilution: dilution factor (already present)

  • Vol_in_well.tube_uL: total volume in well/tube in µL (for spike correction)

  • std: standard reading value

  • extraction: methanol volume ratio = vol added / vol recovered (e.g. 1/0.75 ml)

Cortisol concentration calculations

Input is data with low quality samples flagged, but they get removed before continuing with calculations.

Parameters and unit transformations:

# Define volume of methanol used for cortisol extraction
# vol added / vol recovered (mL)
extraction <- 1.3 / 1

# Reading of spike standard and conversion to ug/dl
std <- (3133 + 3146) / 2 # test 3 backfit
std.r <- std / 10000 # std in ul/dl

# Creating variables in indicated units

df$Buffer_ml <- c(df$Buffer_nl/1000) # dilution (buffer)
df$Ave_Conc_ug.dl <- c(df$Ave_Conc_pg.ml/10000) # Transform to μg/dl from assay output
Wells Sample Category Binding.Perc Ave_Conc_pg.ml Ave_Conc_ug.dl Weight_mg Buffer_ml Spike SpikeVol_ul Dilution TotalVol_well_ul Failed_samples
E5 11 NoSpike 71.6 513.2 0.05132 17.5 0.25 0 0 1 50 NA
F5 12 YesSpike 30.0 2728.0 0.27280 24.1 0.25 1 25 1 50 NA
G5 13 YesSpike 32.1 2477.0 0.24770 16.8 0.25 1 25 1 50 NA

(A) Standard Calculation

Formula:

((A/B) * (C/D) * E * 10,000) = F

  • A = μg/dl from assay output;
  • B = weight (in mg) of hair subjected to extraction;
  • C = vol. (in ml) of methanol added to the powdered hair;
  • D = vol. (in ml) of methanol recovered from the extract and subsequently dried down;
  • E = vol. (in ml) of assay buffer used to reconstitute the dried extract;
  • F = final value of hair CORT Concentration in pg/mg.
##################################
##### Calculate final values #####
##################################

data$Final_conc_pg.mg <- c(
    ((data$Ave_Conc_ug.dl) / data$Weight_mg) *    # A/B *
      extraction *                                # C/D  *     
      data$Buffer_ml * 10000 )                    # E * 10000
Summary of all samples
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.716   7.820  10.531  16.376  15.336  58.971 
Wells Sample Category Binding.Perc Ave_Conc_pg.ml Ave_Conc_ug.dl Weight_mg Buffer_ml Spike SpikeVol_ul Dilution TotalVol_well_ul Failed_samples Final_conc_pg.mg
27 H3 6 YesSpike 34.7 2204.0 0.22040 13.7 0.06 1 25 1 50 NA 12.54832
28 A5 7 YesSpike 30.5 2669.0 0.26690 16.4 0.06 1 25 1 50 NA 12.69402
29 B5 8 NoSpike 77.8 386.8 0.03868 15.3 0.25 0 0 1 50 NA 8.21634
30 C5 9 YesSpike 30.3 2693.0 0.26930 19.2 0.25 1 25 1 50 NA 45.58464

(B) Accounting for Spike

We followed the procedure described in Nist et al. 2020:

“Thus, after pipetting 25μL of standards and samples into the appropriate wells of the 96-well assay plate, we added 25μL of the 0.333ug/dL standard to all samples, resulting in a 1:2 dilution of samples. The remainder of the manufacturer’s protocol was unchanged. We analyzed the assay plate in a Powerwave plate reader (BioTek, Winooski, VT) at 450nm and subtracted background values from all assay wells. In the calculations, we subtracted the 0.333ug/dL standard reading from the sample readings. Samples that resulted in a negative number were considered nondetectable. We converted cortisol levels from ug/dL, as measured by the assay, to pg/mg—based on the mass of hair collected and analyzed using the following formula:

A/B * C/D * E * 10,000 * 2 = F

where - A = μg/dl from assay output; - B = weight (in mg) of collected hair; - C = vol. (in ml) of methanol added to the powdered hair; - D = vol. (in ml) of methanol recovered from the extract and subsequently dried down; - E = vol. (in ml) of assay buffer used to reconstitute the dried extract; 10,000 accounts for changes in metrics; 2 accounts for the dilution factor after addition of the spike; and - F = final value of hair cortisol concentration in pg/mg”

##################################
##### Calculate final values #####
##################################

dSpike$Final_conc_pg.mg <- 
  ifelse(
    dSpike$Spike == 1,                     ## Only spiked samples
      ((dSpike$Ave_Conc_ug.dl - (std.r)) / # (A-spike) 
        dSpike$Weight_mg)                  # / B
        * extraction *                     # C / D
        dSpike$Buffer_ml * 10000 * 2,      # E * 10000 * 2
        dSpike$Final_conc_pg.mg  
    )
Summary of all samples
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
-29.933  -9.370   4.328  -0.182   9.944  11.763 
Summary without spiked samples
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.716   5.087   8.874   7.908  10.486  11.763 
Wells Sample Category Binding.Perc Ave_Conc_pg.ml Ave_Conc_ug.dl Weight_mg Buffer_ml Spike SpikeVol_ul Dilution TotalVol_well_ul Failed_samples Final_conc_pg.mg
28 A5 7 YesSpike 30.5 2669.0 0.26690 16.4 0.06 1 25 1 50 NA -4.475488
29 B5 8 NoSpike 77.8 386.8 0.03868 15.3 0.25 0 0 1 50 NA 8.216340
30 C5 9 YesSpike 30.3 2693.0 0.26930 19.2 0.25 1 25 1 50 NA -15.115885

(C) Sam’s calculation

Developed using Sam’s advice and logic. To facilitate the understanding of what is going on, here I do not transform the output values from pg/ml to ug/dL (as done in A and B).

  • Step 1: Calculate contribution of the spike
  • Step 2: Substract spike from plate reading values and calculate final values accounting for dilution of the sample, weight, and reconstitution

Step 1: Calculate contribution of spike

X * Y / Z / SPd = SP

  • SP = final value of spike contribution in pg/mL
  • X = volume of spike added (mL)
  • Y = concentration of the spike added (pg/mL)
  • SPd = if serially diluted, dilution factor for the spike (i.e: 1, 2, 4, 8, etc.)
  • Z = total volume (mL) in the well or tube, if spike is added before loading the plate (sample + spike)
# Transforming units
data$SpikeVol_ml <- data$SpikeVol_ul/1000           # X to mL
data$TotalVol_well_ml <- data$TotalVol_well_ul/1000 # Z to mL
      # SPd = dilution (in this case, is 1 for all)

 # Calculate spike contribution to each sample
      ##  ( Spike vol. x Spike Conc.)
      ##   ------------------------  / dilution = Spike contribution
      ##        Total vol. 

data$Spike.cont_pg.ml <- (((data$SpikeVol_ml * std ) / # X * Y /
                            data$TotalVol_well_ml) /   # Z /
                              data$Dilution)           # SPd 
summary(data$Spike.cont_pg.ml)
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
    0.0     0.0     0.0   627.9  1569.8  1569.8 
The reading for standard 1 in this plate is 3139.5
The total contribution of the Spike to each sample is 1569.75 pg/mL

Step 2 : Substract spike and calculate final values

((A - SP)/B) * (C/D) * E * SLd = F

  • A = pg/ml from assay output;
  • SP = spike contribution (in pg/ml)
  • B = weight (in mg) of hair subjected to extraction;
  • C = vol. (in ml) of methanol added to the powdered hair;
  • D = vol. (in ml) of methanol recovered from the extract and subsequently dried down;
  • E = vol. (in ml) of assay buffer used to reconstitute the dried extract;
  • SLd = Sample dilution factor (if serially diluted)
  • F = final value of hair CORT Concentration in pg/mg.
##################################
##### Calculate final values #####
##################################
dSpiked$Final_conc_pg.mg <- 
   ((dSpiked$Ave_Conc_pg.ml - dSpiked$Spike.cont_pg.ml) / # (A - spike) 
   dSpiked$Weight_mg) *                                   # / B *
   extraction *                                           # C / D
   dSpiked$Buffer_ml * dSpiked$Dilution                   # E * Sample dilution
dSpiked[ , c("Ave_Conc_pg.ml", "Buffer_ml","Spike.cont_pg.ml", "Final_conc_pg.mg")]
   Ave_Conc_pg.ml Buffer_ml Spike.cont_pg.ml Final_conc_pg.mg
1           513.2      0.25             0.00         9.530857
2          2728.0      0.25          1569.75        15.619554
3          2477.0      0.25          1569.75        17.550967
4          2504.0      0.25          1569.75        22.002264
5           643.6      0.06             0.00         4.183400
6          3196.0      0.06          1569.75         5.420833
7           955.4      0.25             0.00        10.081331
8          3730.0      0.06          1569.75         6.039409
9          2540.0      0.25          1569.75        11.261830
10         2377.0      0.25          1569.75        12.202616
11          793.6      0.25             0.00        10.484553
12          680.2      0.25             0.00        10.836520
13         1991.0      0.06             0.00         7.688020
14         1393.0      0.06             0.00         5.030278
15          839.7      0.25             0.00        11.763039
16         2072.0      0.06             0.00         4.427836
17         2287.0      0.06          1569.75         5.085955
18         2888.0      0.25          1569.75        14.474029
19         1149.0      0.06             0.00         4.227453
20         1197.0      0.25             0.00        10.485849
21         1100.0      0.25             0.00        10.576923
22         1124.0      0.25             0.00        10.290141
23         1062.0      0.25             0.00        11.062500
24         2076.0      0.06             0.00         5.257403
25         2444.0      0.06             0.00         5.493718
26          501.4      0.06             0.00         2.715917
27         2204.0      0.06          1569.75         3.611058
28         2669.0      0.06          1569.75         5.228140
29          386.8      0.25             0.00         8.216340
30         2693.0      0.25          1569.75        19.013346
Summary for all samples:
   Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
  2.716   5.235   9.806   9.329  11.212  22.002 
Sample Final_conc_pg.mg Ave_Conc_pg.ml Spike.cont_pg.ml Binding.Perc Weight_mg Buffer_ml SpikeVol_ul Dilution TotalVol_well_ul
21 33 10.576923 1100.0 0.00 52.3 33.8 0.25 0 1 50
22 34 10.290141 1124.0 0.00 51.7 35.5 0.25 0 1 50
23 36 11.062500 1062.0 0.00 53.2 31.2 0.25 0 1 50
24 37 5.257403 2076.0 0.00 36.1 30.8 0.06 0 1 50
25 38 5.493718 2444.0 0.00 32.5 34.7 0.06 0 1 50
26 5 2.715917 501.4 0.00 72.1 14.4 0.06 0 1 50
27 6 3.611058 2204.0 1569.75 34.7 13.7 0.06 25 1 50
28 7 5.228140 2669.0 1569.75 30.5 16.4 0.06 25 1 50
29 8 8.216340 386.8 0.00 77.8 15.3 0.25 0 1 50
30 9 19.013346 2693.0 1569.75 30.3 19.2 0.25 25 1 50

Plots

(A) Standard Calculation

Final cortisol concentrations not accounting for spike. Tags are sample numbers.

Expected results: a straight horizontal line showing that I obtained same cortisol concentration value in the Y axis, across different sample weights.

Version Author Date
7240d2e Paloma 2025-04-22
16ce91c Paloma 2025-04-10

(B) Accounting for Spike

Final cortisol concentrations accounting for Spike as instructed in Nist et al. 2020.

Expected results: lower values than in the previous plot for the spiked samples, but not as low as negative samples (for all of them). Spiked and non-spiked samples should be aligned (same concentration across different weights)

(C) Sam’s calculation

Final cortisol concentration values using new method.

Expected results: one unique horizontal line, regardless of the spiking status and dilution. We see this line for the spiked samples that were reconstituted using 60 uL (i.e, the most concentrated samples). Perhaps the 250uL samples, by being more diluted and having a larger volume, present more variation if the cort distribution within the well/tube is not homogeneous.
Note that samples seem to be less aligned or more separated from each other than in previous plots. This is due to a difference in scale (A has values 0 to 60, while here all values fall between 2.5 and 22.5).

Evaluation using method C

Version Author Date
7240d2e Paloma 2025-04-22

The previous figure shows that:

  • results are very stable across weights, particularly for the samples where a dilution of 250 uL was used
  • there is more error when using a dilution of 60 uL
  • dilution affects estimation of cortisol concentration in a significant way: even though final concentration numbers account for differences in the dilutions, the results we observe for each group do not overlap
  • the average value when using 250 uL of buffer is twice as big as when using 60 uL
         1          2          3          4          5          6          7 
 0.2480331  6.2865613  8.2734641 12.7475653 -5.0576169 -3.9068384  0.6974098 
         8          9         10         11         12         13         14 
-3.3224690  1.8991926  2.8893870  1.1477595  1.5316518 -1.6153278 -4.2837116 
        15         16         17         18         19         20         21 
 2.4368873 -4.9994132 -4.1474610  5.0992289 -5.0834960  1.0540394  1.1701978 
        22         23         24         25         26         27         28 
 0.8704933  1.6755381 -4.1265188 -3.9198489 -6.5433433 -5.6428807 -4.0463224 
        29         30 
-1.0497613  9.7176001 
         2          3          4          6          8          9         10 
 3.9860988  6.2660887 10.8606365 -6.1791967 -5.7754974 -0.5578506  0.6933117 
        17         18         27         28         30 
-5.9219728  2.5779474 -7.5257946 -6.0376383  7.6138672 
         1          5          7         11         12         13         14 
 2.4895362 -2.2691305  1.6162080  2.6831570  3.4847456  0.3576563 -2.4499596 
        15         16         19         20         21         22         23 
 4.1115169 -4.6474885 -3.2099635  1.3462932  1.7906415  1.3218695  2.5545557 
        24         25         26         29 
-3.2077206 -3.3889115 -3.9935406  1.4105351 

Optimal dilution (using method C results)

Error using samples w/0.06 mL buffer

Mean Absolute Error (MAE) 0.06 mL: 0.803 
Standard Deviation of Residuals 0.06 mL: 1.153 

Error using samples w/0.25 mL buffer

Mean Absolute Error (MAE) 0.25 mL: 2.496 
Standard Deviation of Residuals 0.25 mL: 3.383 

From this we conclude that using a 60 uL dilution produces more accurate/more consistent results

Error using spiked samples only

Mean Absolute Error (MAE) ALL: 5.333 
Standard Deviation of Residuals ALL: 6.312 

Error using non-spiked samples only

Mean Absolute Error (MAE) ALL: 2.574 
Standard Deviation of Residuals ALL: 2.882 

Error using all samples

Mean Absolute Error (MAE) ALL: 3.85 
Standard Deviation of Residuals ALL: 4.858 

sessionInfo()
R version 4.5.0 (2025-04-11)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.4.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Detroit
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] dplyr_1.1.4     paletteer_1.6.0 broom_1.0.8     ggplot2_3.5.2  
[5] knitr_1.50     

loaded via a namespace (and not attached):
 [1] sass_0.4.10       generics_0.1.3    tidyr_1.3.1       lattice_0.22-6   
 [5] stringi_1.8.7     digest_0.6.37     magrittr_2.0.3    evaluate_1.0.3   
 [9] grid_4.5.0        fastmap_1.2.0     Matrix_1.7-3      rprojroot_2.0.4  
[13] workflowr_1.7.1   jsonlite_2.0.0    whisker_0.4.1     backports_1.5.0  
[17] rematch2_2.1.2    promises_1.3.2    mgcv_1.9-1        purrr_1.0.4      
[21] scales_1.3.0      jquerylib_0.1.4   cli_3.6.4         rlang_1.1.6      
[25] munsell_0.5.1     splines_4.5.0     withr_3.0.2       cachem_1.1.0     
[29] yaml_2.3.10       tools_4.5.0       colorspace_2.1-1  httpuv_1.6.16    
[33] vctrs_0.6.5       R6_2.6.1          lifecycle_1.0.4   git2r_0.36.2     
[37] stringr_1.5.1     fs_1.6.6          pkgconfig_2.0.3   pillar_1.10.2    
[41] bslib_0.9.0       later_1.4.2       gtable_0.3.6      glue_1.8.0       
[45] Rcpp_1.0.14       xfun_0.52         tibble_3.2.1      tidyselect_1.2.1 
[49] rstudioapi_0.17.1 farver_2.1.2      nlme_3.1-168      htmltools_0.5.8.1
[53] rmarkdown_2.29    labeling_0.4.3    compiler_4.5.0