Last updated: 2025-04-28

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Knit directory: HairCort-Evaluation-Nist2020/

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File	Version	Author	Date	Message
html	cb56a96	Paloma	2025-04-25	more figures
html	8108c43	Paloma	2025-04-25	improved figures
Rmd	0ed450f	Paloma	2025-04-25	updated input (myassays.com) including dilution
html	0ed450f	Paloma	2025-04-25	updated input (myassays.com) including dilution
html	dd200fc	Paloma	2025-04-23	corrected figures
Rmd	7240d2e	Paloma	2025-04-22	organized files
html	7240d2e	Paloma	2025-04-22	organized files
html	bbb70a9	Paloma	2025-04-09	comparing methods
Rmd	ccad031	Paloma	2025-04-09	new_calc
html	ccad031	Paloma	2025-04-09	new_calc
Rmd	77c2ab5	Paloma	2025-04-08	cleaning test3
html	77c2ab5	Paloma	2025-04-08	cleaning test3

Here I show how files are loaded, merged, and cleaned, including the exclusion of unnecessary columns and handling of missing values.

Summary

Intra-Assay CV: 11.35 %
Intra-Assay CV after removing low quality data: 5.799 %
Good quality data points: 30

# DATA SET 
current_test <- "Test3"
data_path <- file.path("./data", current_test)

Set parameters

# flag samples with high CV (15%) or binding above 80% and under 20%
CV_threshold <- 15.0
uppBinLim <- 80.0
lowBinLim <- 20.0

Data Cleaning and QC

Load, inspect and merge 3 files:

layout: 7 columns (Wells, Sample, weight_mg, buffer_nl, spike, volume of the spike, dilution factor), 96 rows
results: from myassays.com (not including standards)
info: (Wells, Sample, Categ, TotalVol_well_uL)

Merged data set:

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	Sample_comparable
1	C3	0.959	77.3	461.9	396.6	23.30	92.4	65.3	NoSpike	13.1	250	0	50	0	1	13
10	D5	0.743	37.6	940.7	3064.0	98.00	3000.0	2120.0	YesSpike	17.7	60	1	50	25	1	3
11	E5	0.939	71.6	496.8	513.2	4.50	23.1	16.3	NoSpike	17.5	250	0	50	0	1	14
12	F5	0.422	30.0	2690	2728.0	1.92	52.5	37.1	YesSpike	24.1	250	1	50	25	1	17
13	G5	0.451	32.1	2412	2477.0	3.68	91.1	64.4	YesSpike	16.8	250	1	50	25	1	14
14	H5	0.437	31.8	2541	2504.0	2.11	52.9	37.4	YesSpike	13.8	250	1	50	25	1	13

Duplicates with high CV

Flag samples with high coefficient of variation (duplicate measurements that are too different from each other)

High CV in a total of 7 duplicates. These are:

Samples outside the curve

Samples that have a binding percentage over 80 or 20 do not provide accurate results

Total samples outside the curve: 3

Total samples failed

Number of failed samples is 9

Number of good quality data points is 30

Location

Data set with low quality samples flagged saved in: Data_QC_flagged.csv

Good quality data is stored in Data_QC_filtered.csv file

Overall quality of the assay

Intra-Assay CV including all samples is 11.35518 %

Intra-Assay CV including only good quality data is 5.799733 %

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 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

QC_ELISA 3

2025-04-02

Set parameters

Data Cleaning and QC

Duplicates with high CV

Samples outside the curve

Total samples failed