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HairCort-Evaluation-Nist2020/
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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.
# DATA SET
current_test <- "Test3"
data_path <- file.path("./data", current_test)# 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] 98 2| Wells | Sample |
|---|---|
| A1 | NSB |
| A2 | NSB |
| B1 | STD1 |
| B2 | STD1 |
| C1 | STD2 |
| C2 | STD2 |
[1] 82 8| Wells | Raw | X. | Conc. | Conc….Average. | X.CV | SD | SEM |
|---|---|---|---|---|---|---|---|
| A3 | 0.403 | 28.8 | 2899 | 2888.0 | 0.565 | 16.3 | 11.5 |
| A4 | 0.405 | NA | 2876 | NA | NA | NA | NA |
| B3 | 1.050 | 81.1 | 314.1 | 324.9 | 4.700 | 15.3 | 10.8 |
| B4 | 1.040 | NA | 335.7 | NA | NA | NA | NA |
| C3 | 0.959 | 77.3 | 461.9 | 396.6 | 23.300 | 92.4 | 65.3 |
| C4 | 1.040 | NA | 331.3 | NA | NA | NA | NA |
| Wells | Sample | Categ | weight_mg | buffer_nl | spike | vol_in_well.tube_uL | spike_vol_uL | Dilution |
|---|---|---|---|---|---|---|---|---|
| C3 | 1 | NoSpike | 13.1 | 250 | 0 | 50 | 0 | 1 |
| D3 | 2 | NoSpike | 17.2 | 60 | 0 | 50 | 0 | 1 |
| F3 | 4 | NoSpike | 11.7 | 250 | 0 | 50 | 0 | 1 |
| G3 | 5 | NoSpike | 14.4 | 60 | 0 | 50 | 0 | 1 |
| B5 | 8 | NoSpike | 15.3 | 250 | 0 | 50 | 0 | 1 |
| E5 | 11 | NoSpike | 17.5 | 250 | 0 | 50 | 0 | 1 |
# Merge files
m <- merge(layout, results, by = "Wells")
m <- merge(m, info, by = c("Sample", "Wells"))
m <- na.omit(m)
colnames(m) <- c("Sample", "Wells", "Raw.OD",
"Binding.Perc", "Conc_pg.ml",
"Ave_Conc_pg.ml", "CV.Perc",
"SD", "SEM", "Category", "Weight_mg", "Buffer_nl",
"Spike", "TotalVol_well_uL", "SpikeVol_uL", "Dilution")
#m[, 3:11] <- lapply(m[, 3:11],
# function(x) as.numeric(as.character(x)))
m <- m[order(m$Sample),]
kable(head(m)) | Sample | Wells | Raw.OD | Binding.Perc | Conc_pg.ml | Ave_Conc_pg.ml | CV.Perc | SD | SEM | Category | Weight_mg | Buffer_nl | Spike | TotalVol_well_uL | SpikeVol_uL | Dilution |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | C3 | 0.959 | 77.3 | 461.9 | 396.6 | 23.30 | 92.4 | 65.3 | NoSpike | 13.1 | 250 | 0 | 50 | 0 | 1 |
| 10 | D5 | 0.743 | 37.6 | 940.7 | 3064.0 | 98.00 | 3000.0 | 2120.0 | YesSpike | 17.7 | 60 | 1 | 50 | 25 | 1 |
| 11 | E5 | 0.939 | 71.6 | 496.8 | 513.2 | 4.50 | 23.1 | 16.3 | NoSpike | 17.5 | 250 | 0 | 50 | 0 | 1 |
| 12 | F5 | 0.422 | 30.0 | 2690 | 2728.0 | 1.92 | 52.5 | 37.1 | YesSpike | 24.1 | 250 | 1 | 50 | 25 | 1 |
| 13 | G5 | 0.451 | 32.1 | 2412 | 2477.0 | 3.68 | 91.1 | 64.4 | YesSpike | 16.8 | 250 | 1 | 50 | 25 | 1 |
| 14 | H5 | 0.437 | 31.8 | 2541 | 2504.0 | 2.11 | 52.9 | 37.4 | YesSpike | 13.8 | 250 | 1 | 50 | 25 | 1 |
Identify and flag samples with high coefficient of variation (duplicate measurements that are too different from each other)
| Sample | Wells | Raw.OD | Binding.Perc | Conc_pg.ml | Ave_Conc_pg.ml | CV.Perc | SD | SEM | Category | Weight_mg | Buffer_nl | Spike | TotalVol_well_uL | SpikeVol_uL | Dilution | CV_categ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 10 | D5 | 0.743 | 37.6 | 940.7 | 3064.0 | 98.0 | 3000.0 | 2120.0 | YesSpike | 17.7 | 60 | 1 | 50 | 25 | 1 | HIGH CV |
| 25_S | C9 | 0.347 | 31.1 | 3683 | 2802.0 | 44.5 | 1250.0 | 881.0 | DONOTUSE | 37.4 | 60 | 1 | 50 | 25 | 1 | HIGH CV |
| 35 | D11 | 0.548 | 33.8 | 1727 | 2443.0 | 41.5 | 1010.0 | 716.0 | NoSpike | 32.1 | 60 | 0 | 50 | 0 | 1 | HIGH CV |
| 1 | C3 | 0.959 | 77.3 | 461.9 | 396.6 | 23.3 | 92.4 | 65.3 | NoSpike | 13.1 | 250 | 0 | 50 | 0 | 1 | HIGH CV |
| 20 | F7 | 0.538 | 43.6 | 1785 | 1550.0 | 21.4 | 332.0 | 235.0 | NoSpike | 30.1 | 60 | 0 | 50 | 0 | 1 | HIGH CV |
| 4 | F3 | 1.070 | 80.6 | 295.8 | 334.5 | 16.3 | 54.6 | 38.6 | NoSpike | 11.7 | 250 | 0 | 50 | 0 | 1 | HIGH CV |
| 2 | D3 | 0.675 | 53.8 | 1159 | 1045.0 | 15.3 | 160.0 | 113.0 | NoSpike | 17.2 | 60 | 0 | 50 | 0 | 1 | HIGH CV |
High CV in a total of 7 duplicates Wells
1 D5
2 C9
3 D11
4 C3
5 F7
6 F3
7 D3Samples 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: 3| Sample | Wells | Raw.OD | Binding.Perc | Conc_pg.ml | Ave_Conc_pg.ml | CV.Perc | SD | SEM | Category | Weight_mg | Buffer_nl | Spike | TotalVol_well_uL | SpikeVol_uL | Dilution | CV_categ | Binding.Perc_categ | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9 | 17 | C7 | 1.08 | 84.3 | 278 | 270.6 | 3.86 | 10.5 | 7.39 | NoSpike | 24.5 | 60 | 0 | 50 | 0 | 1 | NA | ABOVE 80% binding |
| 25 | 30B | B3 | 1.05 | 81.1 | 314.1 | 324.9 | 4.70 | 15.3 | 10.80 | NoSpike | 29.6 | 250 | 0 | 50 | 0 | 1 | NA | ABOVE 80% binding |
| 34 | 4 | F3 | 1.07 | 80.6 | 295.8 | 334.5 | 16.30 | 54.6 | 38.60 | NoSpike | 11.7 | 250 | 0 | 50 | 0 | 1 | HIGH CV | ABOVE 80% binding |
| Sample | Wells | Raw.OD | Binding.Perc | Conc_pg.ml | Ave_Conc_pg.ml | CV.Perc | SD | SEM | Category | Weight_mg | Buffer_nl | Spike | TotalVol_well_uL | SpikeVol_uL | Dilution | CV_categ | Binding.Perc_categ | Failed_samples | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 34 | 4 | F3 | 1.070 | 80.6 | 295.8 | 334.5 | 16.30 | 54.6 | 38.6 | NoSpike | 11.7 | 250 | 0 | 50 | 0 | 1 | HIGH CV | ABOVE 80% binding | HIGH CV;ABOVE 80% binding |
| 35 | 5 | G3 | 0.944 | 72.1 | 488 | 501.4 | 3.79 | 19.0 | 13.4 | NoSpike | 14.4 | 60 | 0 | 50 | 0 | 1 | NA | NA | NA |
| 36 | 6 | H3 | 0.490 | 34.7 | 2099 | 2204.0 | 6.75 | 149.0 | 105.0 | YesSpike | 13.7 | 60 | 1 | 50 | 25 | 1 | NA | NA | NA |
| 37 | 7 | A5 | 0.436 | 30.5 | 2551 | 2669.0 | 6.25 | 167.0 | 118.0 | YesSpike | 16.4 | 60 | 1 | 50 | 25 | 1 | NA | NA | NA |
| 38 | 8 | B5 | 1.030 | 77.8 | 354.9 | 386.8 | 11.70 | 45.1 | 31.9 | NoSpike | 15.3 | 250 | 0 | 50 | 0 | 1 | NA | NA | NA |
| 39 | 9 | C5 | 0.432 | 30.3 | 2590 | 2693.0 | 5.46 | 147.0 | 104.0 | YesSpike | 19.2 | 250 | 1 | 50 | 25 | 1 | NA | NA | NA |
Data set with low quality samples flagged: Data_QC_flagged.csvNumber of failed samples is 9Number of good quality data points is 30Good 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