Last updated: 2025-06-09
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HairCort-Evaluation-Nist2020/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| html | 22327df | Paloma | 2025-04-28 | elisa5 design |
| html | 8108c43 | Paloma | 2025-04-25 | improved figures |
| Rmd | 0ed450f | Paloma | 2025-04-25 | updated input (myassays.com) including dilution |
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| Rmd | 16ce91c | Paloma | 2025-04-10 | recalc_evaluations |
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| Rmd | ccad031 | Paloma | 2025-04-09 | new_calc |
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Here I show how files are loaded, merged, and cleaned, including the exclusion of unnecessary columns and handling of missing values.
Intra-Assay CV: 11.28 %
Intra-Assay CV after removing low quality data: 4.76 %
Good quality data points: 19
# 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:
Merged dataset:
| Wells | Sample | Category | Weight_mg | Buffer_nl | Spike | SpikeVol_ul | Dilution_spike | Vol_in_well.tube_ul | Extraction_ratio | Dilution_sample | Raw.OD | Binding.Perc | Conc_pg.ml | Ave_Conc_pg.ml | CV.Perc | SD | SEM | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 36 | D3 | TA1 | A | 50 | 250 | 0 | 0 | 1 | 50 | 1.351351 | 1 | 0.185 | NA | 4508.0 | NA | NA | NA | NA |
| 46 | E3 | TA2 | A | 50 | 250 | 0 | 0 | 1 | 50 | 1.351351 | 2 | 0.274 | 22.5 | 2616.0 | 2932.0 | 15.20 | 446.0 | 315.0 |
| 56 | F3 | TA2 | A | 50 | 250 | 0 | 0 | 1 | 50 | 1.351351 | 2 | 0.236 | NA | 3247.0 | NA | NA | NA | NA |
| 66 | G3 | TA3 | A | 50 | 250 | 0 | 0 | 1 | 50 | 1.351351 | 4 | 0.439 | 44.1 | 1186.0 | 1139.0 | 5.85 | 66.6 | 47.1 |
| 6 | A4 | TA4 | A | 50 | 250 | 0 | 0 | 1 | 50 | 1.351351 | 8 | 0.554 | 54.9 | 724.6 | 753.4 | 5.41 | 40.7 | 28.8 |
| 7 | A5 | TB1 | B | 50 | 250 | 1 | 25 | 1 | 275 | 1.333333 | 1 | 0.160 | 12.2 | 5415.0 | 5334.0 | 2.16 | 115.0 | 81.6 |
| 38 | D5 | TB2 | B | 50 | 250 | 1 | 25 | 2 | 250 | 1.333333 | 2 | 0.272 | NA | 2645.0 | NA | NA | NA | NA |
| 48 | E5 | TB3 | B | 50 | 250 | 1 | 25 | 4 | 250 | 1.333333 | 4 | 0.457 | 45.8 | 1097.0 | 1067.0 | 3.97 | 42.4 | 30.0 |
Flag samples with high coefficient of variation (duplicate measurements that are too different from each other)
High CV in a total of 10 duplicates. These are: Sample
1 B0
2 BE
3 TA7
4 TC6
5 TB7
6 TA6
7 TP1B
8 TC7
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 (some are blanks or NSB)| Wells | Sample | Category | Weight_mg | Buffer_nl | Spike | SpikeVol_ul | Dilution_spike | Vol_in_well.tube_ul | Extraction_ratio | Dilution_sample | 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 | 50 | 1.351351 | 1 | 0.258 | 23.0 | 2859 | 2843 | 0.795 | 22.6 | 16 | NA | NA | NA |
| 74 | H11 | TP3A | P | 12 | 220 | 1 | 25 | 1 | 50 | 1.351351 | 1 | 0.260 | NA | 2827 | NA | NA | NA | NA | NA | NA | NA |
| 4 | A12 | TP3B | P | 12 | 60 | 1 | 25 | 1 | 50 | 1.333333 | 1 | 0.196 | 15.6 | 4180 | 4282 | 3.370 | 144.0 | 102 | NA | UNDER 20% binding | UNDER 20% binding |
| 15 | B12 | TP3B | P | 12 | 60 | 1 | 25 | 1 | 50 | 1.333333 | 1 | 0.189 | NA | 4384 | NA | NA | NA | NA | NA | NA | NA |
| 25 | C12 | TP3C | P | 12 | 60 | 1 | 25 | 1 | 50 | 1.333333 | 1 | 0.181 | 13.6 | 4636 | 4866 | 6.680 | 325.0 | 230 | NA | UNDER 20% binding | UNDER 20% binding |
| 35 | D12 | TP3C | P | 12 | 60 | 1 | 25 | 1 | 50 | 1.333333 | 1 | 0.168 | NA | 5096 | NA | NA | NA | NA | NA | NA | NA |
Number of failed samples is 22Number of good quality data points is 19Location
Good quality data is stored in Data_QC_filtered.csv fileData set with low quality samples flagged: Data_QC_flagged.csvOverall quality of the assay
Intra-Assay CV including all samples is 12.05 %Intra-Assay CV including only good quality data is 4.97 %, for a total of 19 samples
sessionInfo()R version 4.5.0 (2025-04-11)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5
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 knitr_1.50
loaded via a namespace (and not attached):
[1] vctrs_0.6.5 cli_3.6.4 rlang_1.1.6 xfun_0.52
[5] stringi_1.8.7 generics_0.1.3 promises_1.3.2 jsonlite_2.0.0
[9] workflowr_1.7.1 glue_1.8.0 rprojroot_2.0.4 git2r_0.36.2
[13] htmltools_0.5.8.1 httpuv_1.6.16 sass_0.4.10 rmarkdown_2.29
[17] evaluate_1.0.3 jquerylib_0.1.4 tibble_3.2.1 fastmap_1.2.0
[21] yaml_2.3.10 lifecycle_1.0.4 whisker_0.4.1 stringr_1.5.1
[25] compiler_4.5.0 fs_1.6.6 Rcpp_1.0.14 pkgconfig_2.0.3
[29] rstudioapi_0.17.1 later_1.4.2 digest_0.6.37 R6_2.6.1
[33] tidyselect_1.2.1 pillar_1.10.2 magrittr_2.0.3 bslib_0.9.0
[37] tools_4.5.0 cachem_1.1.0