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HairCort-Evaluation-Nist2020/
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| html | bbb70a9 | Paloma | 2025-04-09 | comparing methods |
| Rmd | ccad031 | Paloma | 2025-04-09 | new_calc |
| html | ccad031 | Paloma | 2025-04-09 | new_calc |
| html | ca6c804 | Paloma | 2025-04-03 | new calc final vals |
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| html | 528855b | Paloma | 2025-04-03 | new_calc |
Data Cleaning and Quality Control (QC) details how files are loaded, merged, and cleaned, including the exclusion of unnecessary columns and handling of missing values.
# flag samples with high CV (15%) or binding above 80% and under 20%
CV_threshold <- 15.0
uppBinLim <- 80.0
lowBinLim <- 20.0Load, inspect and merge 3 files:
[1] 96 11| Wells | Sample | Categ | weight_mg | buffer_nl | spike | spike_vol_uL | Dilution_sample | Dilution_spike | vol_in_well.tube_uL | Extraction_ratio |
|---|---|---|---|---|---|---|---|---|---|---|
| A3 | B0 | b0 | . | NA | 0 | 0 | 1 | 1 | NA | NA |
| B3 | B0 | b0 | . | NA | 0 | 0 | 1 | 1 | NA | NA |
| G12 | BE | be | . | NA | 0 | 0 | 1 | 1 | NA | NA |
| H12 | BE | be | . | NA | 0 | 0 | 1 | 1 | NA | NA |
| A1 | NSB | nsb | . | . | 0 | 0 | 1 | 1 | NA | NA |
| B1 | NSB | nsb | . | . | 0 | 0 | 1 | 1 | NA | NA |
[1] 82 8| Wells | Raw | X. | Conc. | Conc….Average. | X.CV | SD | SEM |
|---|---|---|---|---|---|---|---|
| C3 | 0.171 | 14.0 | 4810 | 4617 | 5.90 | 273.0 | 193.0 |
| D3 | 0.183 | NA | 4425 | NA | NA | NA | NA |
| E3 | 0.272 | 22.4 | 2594 | 2921 | 15.80 | 462.0 | 326.0 |
| F3 | 0.232 | NA | 3247 | NA | NA | NA | NA |
| G3 | 0.435 | 44.3 | 1192 | 1133 | 7.39 | 83.8 | 59.2 |
| H3 | 0.459 | NA | 1074 | NA | NA | NA | NA |
Warning in FUN(X[[i]], ...): NAs introduced by coercion
Warning in FUN(X[[i]], ...): NAs introduced by coercion
Warning in FUN(X[[i]], ...): NAs introduced by coercion
Warning in FUN(X[[i]], ...): NAs introduced by coercion| Wells | Sample | Category | Weight_mg | Buffer_nl | Spike | SpikeVol_uL | Dilution_sample | Dilution_spike | Vol_in_well.tube_uL | Extraction_ratio | Raw.OD | Binding.Perc | Conc_pg/ml | Ave_Conc_pg/ml | CV.Perc | SD | SEM | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 64 | G11 | TP3A | P | 12 | 220 | 1 | 25 | 1 | 1 | 50 | 1.351351 | 0.258 | 23.2 | 2800 | 2792 | 0.391 | 10.9 | 7.71 |
| 74 | H11 | TP3A | P | 12 | 220 | 1 | 25 | 1 | 1 | 50 | 1.351351 | 0.259 | NA | 2785 | NA | NA | NA | NA |
| 4 | A12 | TP3B | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.195 | 15.5 | 4084 | 4210 | 4.230 | 178.0 | 126.00 |
| 15 | B12 | TP3B | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.186 | NA | 4336 | NA | NA | NA | NA |
| 25 | C12 | TP3C | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.186 | 13.9 | 4336 | 4661 | 9.870 | 460.0 | 325.00 |
| 35 | D12 | TP3C | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.166 | NA | 4986 | NA | NA | NA | NA |
Identify and flag samples with high coefficient of variation (duplicate measurements that are too different from each other)
| Wells | Sample | Category | Weight_mg | Buffer_nl | Spike | SpikeVol_uL | Dilution_sample | Dilution_spike | Vol_in_well.tube_uL | Extraction_ratio | Raw.OD | Binding.Perc | Conc_pg/ml | Ave_Conc_pg/ml | CV.Perc | SD | SEM | CV_categ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A3 | B0 | b0 | NA | NA | 0 | 0 | 1 | 1 | NA | NA | 0.874 | 100.0 | 140.60 | 86.84 | 87.5 | 76.0 | 53.7 | HIGH CV |
| G12 | BE | be | NA | NA | 0 | 0 | 1 | 1 | NA | NA | 0.553 | 70.8 | 717.50 | 462.90 | 77.8 | 360.0 | 255.0 | HIGH CV |
| G4 | TA7 | A | 50 | 250 | 0 | 0 | 64 | 1 | 50 | 1.351351 | 1.010 | 103.0 | 33.09 | 62.13 | 66.1 | 41.1 | 29.0 | HIGH CV |
| E4 | TA6 | A | 50 | 250 | 0 | 0 | 32 | 1 | 50 | 1.351351 | 0.856 | 84.2 | 158.90 | 226.00 | 42.0 | 95.0 | 67.2 | HIGH CV |
| E6 | TB7 | B | 50 | 250 | 1 | 25 | 64 | 64 | 250 | 1.333333 | 0.780 | 87.0 | 249.20 | 194.40 | 39.9 | 77.5 | 54.8 | HIGH CV |
| E10 | TP1B | P | 6 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.254 | 18.1 | 2863.00 | 3820.00 | 35.4 | 1350.0 | 957.0 | HIGH CV |
| C8 | TC7 | C | 50 | 250 | 0 | 0 | 64 | 1 | 250 | 1.481481 | 0.939 | 96.4 | 83.16 | 107.50 | 32.0 | 34.4 | 24.3 | HIGH CV |
| A8 | TC6 | C | 50 | 250 | 0 | 0 | 32 | 1 | 250 | 1.481481 | 0.897 | 97.7 | 118.80 | 97.49 | 30.9 | 30.1 | 21.3 | HIGH CV |
| G7 | TC5 | C | 50 | 250 | 0 | 0 | 16 | 1 | 250 | 1.481481 | 0.842 | 92.0 | 173.80 | 144.50 | 28.7 | 41.5 | 29.3 | HIGH CV |
| E3 | TA2 | A | 50 | 250 | 0 | 0 | 2 | 1 | 50 | 1.351351 | 0.272 | 22.4 | 2594.00 | 2921.00 | 15.8 | 462.0 | 326.0 | HIGH CV |
High CV in a total of 10 duplicates Sample
1 B0
2 BE
3 TA7
4 TA6
5 TB7
6 TP1B
7 TC7
8 TC6
9 TC5
10 TA2Samples that have a binding percentage over 80 or 20 do not provide accurate results, and we consider them to be outside the curve.
Total samples outside the curve: 20| Wells | Sample | Category | Weight_mg | Buffer_nl | Spike | SpikeVol_uL | Dilution_sample | Dilution_spike | Vol_in_well.tube_uL | Extraction_ratio | Raw.OD | Binding.Perc | Conc_pg/ml | Ave_Conc_pg/ml | CV.Perc | SD | SEM | CV_categ | Binding.Perc_categ | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 5 | A3 | B0 | b0 | NA | NA | 0 | 0 | 1 | 1 | NA | NA | 0.874 | 100.0 | 140.60 | 86.84 | 87.500 | 76.000 | 53.70 | HIGH CV | ABOVE 80% binding |
| 1 | A1 | NSB | nsb | NA | NA | 0 | 0 | 1 | 1 | NA | NA | 0.052 | 0.0 | 15610.00 | 15610.00 | 0.000 | 0.000 | 0.00 | NA | UNDER 20% binding |
| 26 | C3 | TA1 | A | 50 | 250 | 0 | 0 | 1 | 1 | 50 | 1.351351 | 0.171 | 14.0 | 4810.00 | 4617.00 | 5.900 | 273.000 | 193.00 | NA | UNDER 20% binding |
| 47 | E4 | TA6 | A | 50 | 250 | 0 | 0 | 32 | 1 | 50 | 1.351351 | 0.856 | 84.2 | 158.90 | 226.00 | 42.000 | 95.000 | 67.20 | HIGH CV | ABOVE 80% binding |
| 67 | G4 | TA7 | A | 50 | 250 | 0 | 0 | 64 | 1 | 50 | 1.351351 | 1.010 | 103.0 | 33.09 | 62.13 | 66.100 | 41.100 | 29.00 | HIGH CV | ABOVE 80% binding |
| 7 | A5 | TB1 | B | 50 | 250 | 1 | 25 | 1 | 1 | 275 | 1.333333 | 0.161 | 12.3 | 5172.00 | 5134.00 | 1.040 | 53.500 | 37.80 | NA | UNDER 20% binding |
| 29 | C6 | TB6 | B | 50 | 250 | 1 | 25 | 32 | 32 | 250 | 1.333333 | 0.830 | 88.2 | 187.30 | 178.90 | 6.590 | 11.800 | 8.34 | NA | ABOVE 80% binding |
| 49 | E6 | TB7 | B | 50 | 250 | 1 | 25 | 64 | 64 | 250 | 1.333333 | 0.780 | 87.0 | 249.20 | 194.40 | 39.900 | 77.500 | 54.80 | HIGH CV | ABOVE 80% binding |
| 70 | G7 | TC5 | C | 50 | 250 | 0 | 0 | 16 | 1 | 250 | 1.481481 | 0.842 | 92.0 | 173.80 | 144.50 | 28.700 | 41.500 | 29.30 | HIGH CV | ABOVE 80% binding |
| 10 | A8 | TC6 | C | 50 | 250 | 0 | 0 | 32 | 1 | 250 | 1.481481 | 0.897 | 97.7 | 118.80 | 97.49 | 30.900 | 30.100 | 21.30 | HIGH CV | ABOVE 80% binding |
| 31 | C8 | TC7 | C | 50 | 250 | 0 | 0 | 64 | 1 | 250 | 1.481481 | 0.939 | 96.4 | 83.16 | 107.50 | 32.000 | 34.400 | 24.30 | HIGH CV | ABOVE 80% binding |
| 51 | E8 | TD1 | D | 20 | 110 | 1 | 110 | 1 | 1 | 220 | 1.333333 | 0.188 | 15.7 | 4278.00 | 4168.00 | 3.740 | 156.000 | 110.00 | NA | UNDER 20% binding |
| 52 | E9 | TD5 | D | 20 | 110 | 1 | 110 | 16 | 16 | 220 | 1.333333 | 0.757 | 80.2 | 281.40 | 268.00 | 7.060 | 18.900 | 13.40 | NA | ABOVE 80% binding |
| 72 | G9 | TD6 | D | 20 | 110 | 1 | 110 | 32 | 32 | 220 | 1.333333 | 0.939 | 99.7 | 83.16 | 81.99 | 2.030 | 1.660 | 1.17 | NA | ABOVE 80% binding |
| 2 | A10 | TD7 | D | 20 | 110 | 1 | 110 | 64 | 64 | 220 | 1.333333 | 0.934 | 99.0 | 87.13 | 86.73 | 0.652 | 0.566 | 0.40 | NA | ABOVE 80% binding |
| 43 | E10 | TP1B | P | 6 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.254 | 18.1 | 2863.00 | 3820.00 | 35.400 | 1350.000 | 957.00 | HIGH CV | UNDER 20% binding |
| 3 | A11 | TP2A | P | 9 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.208 | 17.3 | 3757.00 | 3793.00 | 1.340 | 50.800 | 35.90 | NA | UNDER 20% binding |
| 44 | E11 | TP2C | P | 9 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.219 | 18.1 | 3510.00 | 3634.00 | 4.810 | 175.000 | 124.00 | NA | UNDER 20% binding |
| 4 | A12 | TP3B | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.195 | 15.5 | 4084.00 | 4210.00 | 4.230 | 178.000 | 126.00 | NA | UNDER 20% binding |
| 25 | C12 | TP3C | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.186 | 13.9 | 4336.00 | 4661.00 | 9.870 | 460.000 | 325.00 | NA | UNDER 20% binding |
| Wells | Sample | Category | Weight_mg | Buffer_nl | Spike | SpikeVol_uL | Dilution_sample | Dilution_spike | Vol_in_well.tube_uL | Extraction_ratio | Raw.OD | Binding.Perc | Conc_pg/ml | Ave_Conc_pg/ml | CV.Perc | SD | SEM | CV_categ | Binding.Perc_categ | Failed_samples | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 64 | G11 | TP3A | P | 12 | 220 | 1 | 25 | 1 | 1 | 50 | 1.351351 | 0.258 | 23.2 | 2800 | 2792 | 0.391 | 10.9 | 7.71 | NA | NA | NA |
| 74 | H11 | TP3A | P | 12 | 220 | 1 | 25 | 1 | 1 | 50 | 1.351351 | 0.259 | NA | 2785 | NA | NA | NA | NA | NA | NA | NA |
| 4 | A12 | TP3B | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.195 | 15.5 | 4084 | 4210 | 4.230 | 178.0 | 126.00 | NA | UNDER 20% binding | UNDER 20% binding |
| 15 | B12 | TP3B | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.186 | NA | 4336 | NA | NA | NA | NA | NA | NA | NA |
| 25 | C12 | TP3C | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.186 | 13.9 | 4336 | 4661 | 9.870 | 460.0 | 325.00 | NA | UNDER 20% binding | UNDER 20% binding |
| 35 | D12 | TP3C | P | 12 | 60 | 1 | 25 | 1 | 1 | 50 | 1.333333 | 0.166 | NA | 4986 | NA | NA | NA | NA | NA | NA | NA |
Data set with low quality samples flagged: Data_QC_flagged.csv[1] 22Number of failed samples is 22Number of good quality data points is 19Good quality data is stored in Data_QC_filtered.csv file
sessionInfo()R version 4.4.3 (2025-02-28)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
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 knitr_1.49
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 cli_3.6.3 rlang_1.1.4 xfun_0.49
[5] stringi_1.8.4 generics_0.1.3 promises_1.3.0 jsonlite_1.8.9
[9] workflowr_1.7.1 glue_1.8.0 rprojroot_2.0.4 git2r_0.35.0
[13] htmltools_0.5.8.1 httpuv_1.6.15 sass_0.4.9 fansi_1.0.6
[17] rmarkdown_2.29 jquerylib_0.1.4 evaluate_1.0.1 tibble_3.2.1
[21] fastmap_1.2.0 yaml_2.3.10 lifecycle_1.0.4 whisker_0.4.1
[25] stringr_1.5.1 compiler_4.4.3 fs_1.6.5 Rcpp_1.0.13-1
[29] pkgconfig_2.0.3 rstudioapi_0.17.1 later_1.3.2 digest_0.6.37
[33] R6_2.5.1 tidyselect_1.2.1 utf8_1.2.4 pillar_1.9.0
[37] magrittr_2.0.3 bslib_0.8.0 tools_4.4.3 cachem_1.1.0