Last updated: 2024-10-16
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Knit directory: test-3/
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Attaching package: 'dplyr'The following objects are masked from 'package:stats':
filter, lagThe following objects are masked from 'package:base':
intersect, setdiff, setequal, unionlayout <- read.csv("./data/layout_wells_test3_091524.csv", stringsAsFactors = TRUE, na.strings = c("", " "))
results <- read.csv("./data/myassays_table_test3_091524.csv", stringsAsFactors = TRUE, na.strings = c("", " ", "-"))
info <- read.csv("./data/sample_info_test3_091524.csv", stringsAsFactors = TRUE, na.strings = c("", " "))
#kable(summary(c(layout, results, info)))kable(head(layout)) | Wells | Sample |
|---|---|
| A1 | NSB |
| A2 | NSB |
| B1 | STD1 |
| B2 | STD1 |
| C1 | STD2 |
| C2 | STD2 |
kable(head(results)) | Sample | Wells | Raw | X. | Conc. | Conc….Average. | X.CV | SD | SEM |
|---|---|---|---|---|---|---|---|---|
| Unknown1 | A3 | 0.403 | 28.8 | 2899 | 2888.0 | 0.565 | 16.3 | 11.5 |
| NA | A4 | 0.405 | NA | 2876 | NA | NA | NA | NA |
| Unknown2 | B3 | 1.050 | 81.1 | 314.1 | 324.9 | 4.700 | 15.3 | 10.8 |
| NA | B4 | 1.040 | NA | 335.7 | NA | NA | NA | NA |
| Unknown3 | C3 | 0.959 | 77.3 | 461.9 | 396.6 | 23.300 | 92.4 | 65.3 |
| NA | C4 | 1.040 | NA | 331.3 | NA | NA | NA | NA |
dim(results)[1] 82 9results <- results %>%
select(!Sample)
m <- merge(layout, results, by = "Wells")
kable(head(m)) | Wells | Sample | Raw | X. | Conc. | Conc….Average. | X.CV | SD | SEM |
|---|---|---|---|---|---|---|---|---|
| A1 | NSB | 0.054 | 0.0 | < Curve | NA | NA | NA | NA |
| A10 | 15 | 0.840 | NA | 694.2 | NA | NA | NA | NA |
| A11 | 32 | 0.656 | 50.0 | 1228 | 1197 | 3.690 | 44.2 | 31.3 |
| A12 | 32 | 0.673 | NA | 1166 | NA | NA | NA | NA |
| A2 | NSB | 0.045 | NA | < Curve | NA | NA | NA | NA |
| A3 | 30A | 0.403 | 28.8 | 2899 | 2888 | 0.565 | 16.3 | 11.5 |
dim(m)[1] 82 9m<- merge(m, info, by = c("Sample", "Wells"))
m <- na.omit(m)
kable(head(m)) | Sample | Wells | Raw | X. | Conc. | Conc….Average. | X.CV | SD | SEM | weight_mg | buffer_nl | spike |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | C3 | 0.959 | 77.3 | 461.9 | 396.6 | 23.30 | 92.4 | 65.3 | 13.1 | 250 | 0 |
| 10 | D5 | 0.743 | 37.6 | 940.7 | 3064.0 | 98.00 | 3000.0 | 2120.0 | 17.7 | 60 | 1 |
| 11 | E5 | 0.939 | 71.6 | 496.8 | 513.2 | 4.50 | 23.1 | 16.3 | 17.5 | 250 | 0 |
| 12 | F5 | 0.422 | 30.0 | 2690 | 2728.0 | 1.92 | 52.5 | 37.1 | 24.1 | 250 | 1 |
| 13 | G5 | 0.451 | 32.1 | 2412 | 2477.0 | 3.68 | 91.1 | 64.4 | 16.8 | 250 | 1 |
| 14 | H5 | 0.437 | 31.8 | 2541 | 2504.0 | 2.11 | 52.9 | 37.4 | 13.8 | 250 | 1 |
dim(m)[1] 38 12colnames(m) <- c("Sample", "Wells", "Raw.OD", "Binding.Perc", "Concentration_pg/ml","Average_Conc_pg/ml", "CV.Perc", "SD", "SEM", "Weight_mg", "Buffer_nl", "Spike")
m[, 3:11] <- lapply(m[, 3:11], function(x) as.numeric(as.character(x)))
m$Spike <- as.factor(m$Spike)CV_threshold <- 15.0
cv_high <- m %>%
filter(CV.Perc > CV_threshold) %>%
arrange(desc(CV.Perc))
kable(cv_high)| Sample | Wells | Raw.OD | Binding.Perc | Concentration_pg/ml | Average_Conc_pg/ml | CV.Perc | SD | SEM | Weight_mg | Buffer_nl | Spike |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 10 | D5 | 0.743 | 37.6 | 940.7 | 3064.0 | 98.0 | 3000.0 | 2120.0 | 17.7 | 60 | 1 |
| 35 | D11 | 0.548 | 33.8 | 1727.0 | 2443.0 | 41.5 | 1010.0 | 716.0 | 32.1 | 60 | 0 |
| 1 | C3 | 0.959 | 77.3 | 461.9 | 396.6 | 23.3 | 92.4 | 65.3 | 13.1 | 250 | 0 |
| 20 | F7 | 0.538 | 43.6 | 1785.0 | 1550.0 | 21.4 | 332.0 | 235.0 | 30.1 | 60 | 0 |
| 4 | F3 | 1.070 | 80.6 | 295.8 | 334.5 | 16.3 | 54.6 | 38.6 | 11.7 | 250 | 0 |
| 2 | D3 | 0.675 | 53.8 | 1159.0 | 1045.0 | 15.3 | 160.0 | 113.0 | 17.2 | 60 | 0 |
# flag high CV
m1 <- m %>%
mutate(CV_categ = ifelse(CV.Perc > CV_threshold, "HIGH CV", NA))out_curve <- m %>%
filter(Binding.Perc < 20.0 | Binding.Perc > 80.0) %>%
arrange(desc(Binding.Perc))
kable(out_curve)| Sample | Wells | Raw.OD | Binding.Perc | Concentration_pg/ml | Average_Conc_pg/ml | CV.Perc | SD | SEM | Weight_mg | Buffer_nl | Spike |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 17 | C7 | 1.08 | 84.3 | 278.0 | 270.6 | 3.86 | 10.5 | 7.39 | 24.5 | 60 | 0 |
| 30B | B3 | 1.05 | 81.1 | 314.1 | 324.9 | 4.70 | 15.3 | 10.80 | 29.6 | 250 | 0 |
| 4 | F3 | 1.07 | 80.6 | 295.8 | 334.5 | 16.30 | 54.6 | 38.60 | 11.7 | 250 | 0 |
# flag samples outside the curve
m2 <- m1 %>%
mutate(Binding.Perc_categ = ifelse(Binding.Perc > 80, "ABOVE 80% binding", ifelse(Binding.Perc < 20, "UNDER 20% binding", NA)))
m2 <- m2 %>%
mutate(Failed_samples = ifelse(!is.na(CV_categ) & !is.na(Binding.Perc_categ),
paste(CV_categ, Binding.Perc_categ, sep = ";"),
coalesce(CV_categ, Binding.Perc_categ))) %>%
select(!c(CV_categ, Binding.Perc_categ))
# dataset with problematic samples flagged
kable(head(m2))| Sample | Wells | Raw.OD | Binding.Perc | Concentration_pg/ml | Average_Conc_pg/ml | CV.Perc | SD | SEM | Weight_mg | Buffer_nl | Spike | Failed_samples |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | C3 | 0.959 | 77.3 | 461.9 | 396.6 | 23.30 | 92.4 | 65.3 | 13.1 | 250 | 0 | HIGH CV |
| 10 | D5 | 0.743 | 37.6 | 940.7 | 3064.0 | 98.00 | 3000.0 | 2120.0 | 17.7 | 60 | 1 | HIGH CV |
| 11 | E5 | 0.939 | 71.6 | 496.8 | 513.2 | 4.50 | 23.1 | 16.3 | 17.5 | 250 | 0 | NA |
| 12 | F5 | 0.422 | 30.0 | 2690.0 | 2728.0 | 1.92 | 52.5 | 37.1 | 24.1 | 250 | 1 | NA |
| 13 | G5 | 0.451 | 32.1 | 2412.0 | 2477.0 | 3.68 | 91.1 | 64.4 | 16.8 | 250 | 1 | NA |
| 14 | H5 | 0.437 | 31.8 | 2541.0 | 2504.0 | 2.11 | 52.9 | 37.4 | 13.8 | 250 | 1 | NA |
write.csv(m2, "./data/Data_QC_flagged.csv", row.names = FALSE)
# dataset with high cv samples removed
data.no_cv <- m2 %>%
filter(CV.Perc > CV_threshold)
write.csv(data.no_cv, "./data/Data_QC_filtered.csv", row.names = FALSE)
# table with samples that failed
failed_samples <- rbind(cv_high, out_curve)
write.csv(failed_samples, "./data/failed_samples.csv", row.names = FALSE)
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.5.1 knitr_1.48 dplyr_1.1.2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 pillar_1.9.0 compiler_4.1.0 bslib_0.8.0
[5] later_1.3.0 jquerylib_0.1.4 git2r_0.31.0 workflowr_1.7.1
[9] tools_4.1.0 digest_0.6.31 gtable_0.3.5 jsonlite_1.8.9
[13] evaluate_1.0.0 lifecycle_1.0.4 tibble_3.2.1 pkgconfig_2.0.3
[17] rlang_1.1.0 cli_3.6.1 rstudioapi_0.16.0 yaml_2.3.7
[21] xfun_0.47 fastmap_1.1.1 withr_3.0.1 stringr_1.5.1
[25] generics_0.1.3 fs_1.5.2 vctrs_0.6.5 sass_0.4.9
[29] grid_4.1.0 tidyselect_1.2.0 rprojroot_2.0.4 glue_1.6.2
[33] R6_2.5.1 fansi_1.0.4 rmarkdown_2.28 magrittr_2.0.3
[37] whisker_0.4.1 scales_1.3.0 promises_1.2.0.1 htmltools_0.5.8.1
[41] colorspace_2.1-0 httpuv_1.6.9 utf8_1.2.3 stringi_1.7.12
[45] munsell_0.5.1 cachem_1.0.7