diff --git a/scripts/10_correction_batch_effects_unfiltered.Rmd b/scripts/10_correction_batch_effects_unfiltered.Rmd
index ce10593..fae0021 100644
--- a/scripts/10_correction_batch_effects_unfiltered.Rmd
+++ b/scripts/10_correction_batch_effects_unfiltered.Rmd
@@ -30,6 +30,7 @@ start_time <- Sys.time()
 ```
 
 ```{r setup, include=FALSE}
+source("../data/calculate_pc_cutoff.R") # source function for determining PC cutoff 
 needed_packages <- c("BiocManager", "dplyr", "knitr", "rmarkdown", "tibble", "ggplot2", 
                      "ggrepel", "broom", "gplots", "tidyr", "sva", "methods")
 installed_packages <- needed_packages %in% rownames(installed.packages())
@@ -85,8 +86,8 @@ if (correction_variable_1 == "PLEASE FILL IN"){
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
   
-  R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-  print(paste0(R, " PCs that explained a minimum of >10% change of variance were included"))
+  R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+  print(paste0(R, " PCs were included"))
   
   phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
     select(personid, plate, slide, array, row, column, arrayid)
@@ -244,8 +245,8 @@ if (correction_variable_2 == "PLEASE FILL IN"){
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
   
-  R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-  print(paste0(R, " PCs that explained a minimum of >10% change of variance were included"))
+  R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+  print(paste0(R, " PCs were included"))
   
   phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
     select(personid, plate, slide, array, row, column, arrayid)
@@ -403,8 +404,8 @@ if (correction_variable_3 == "PLEASE FILL IN"){
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
   
-  R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-  print(paste0(R, " PCs that explained >10% change of variance were included"))
+  R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+  print(paste0(R, " PCs were included"))
   
   phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
     select(personid, plate, slide, array, row, column, arrayid)
diff --git a/scripts/8_removal_of_outliers_detect_batch_effects.Rmd b/scripts/8_removal_of_outliers_detect_batch_effects.Rmd
index 81f2c90..6b325a7 100644
--- a/scripts/8_removal_of_outliers_detect_batch_effects.Rmd
+++ b/scripts/8_removal_of_outliers_detect_batch_effects.Rmd
@@ -46,6 +46,7 @@ start_time <- Sys.time()
 
 
 ```{r setup, include=FALSE}
+source("../data/calculate_pc_cutoff.R") # source function for determining PC cutoff 
 needed_packages <- c("BiocManager", "dplyr", "knitr", "rmarkdown", "tibble", "ggplot2", 
                      "ggrepel", "broom", "gplots", "tidyr", "sva", "methods")
 installed_packages <- needed_packages %in% rownames(installed.packages())
@@ -124,8 +125,8 @@ variance_explained %>%
   labs(x = "Principal Component", y = "Portion of variance Explained (%)", title = "Scree Plot",
        subtitle = "Note: cumulative variance explained (%) is displayed as text")
 
-R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-print(paste0(R, " PCs that expained >10% of the variance were included"))
+R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+print(paste0(R, " PCs were included"))
 
 phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
   select(personid, plate, slide, array, row, column, arrayid)
@@ -259,8 +260,8 @@ if(!identical(extreme_outliers_filtered %>% pull(personid),character(0))){
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
   
-  R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-  print(paste0(R, " PCs that expained >10% of the variance were included"))
+  R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+  print(paste0(R, " PCs were included"))
   
   phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
     select(personid, plate, slide, array, row, column, arrayid)
@@ -470,8 +471,8 @@ variance_explained %>%
   labs(x = "Principal Component", y = "Portion of variance Explained (%)", title = "Scree Plot",
        subtitle = "Note: cumulative variance explained (%) is displayed as text")
 
-R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-print(paste0(R, " PCs that expained >10% of the variance were included"))
+R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+print(paste0(R, " PCs were included"))
 
 phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
   select(personid, plate, slide, array, row, column, arrayid)
@@ -606,8 +607,8 @@ if(!identical(extreme_outliers_unfiltered %>% pull(personid),character(0))){
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
   
-  R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-  print(paste0(R, " PCs that expained >10% of the variance were included"))
+  R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+  print(paste0(R, " PCs were included"))
   
   phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
     select(personid, plate, slide, array, row, column, arrayid)
diff --git a/scripts/9_correction_batch_effects_filtered.Rmd b/scripts/9_correction_batch_effects_filtered.Rmd
index 28c4525..2081997 100644
--- a/scripts/9_correction_batch_effects_filtered.Rmd
+++ b/scripts/9_correction_batch_effects_filtered.Rmd
@@ -41,6 +41,7 @@ start_time <- Sys.time()
 ```
 
 ```{r setup, include=FALSE}
+source("../data/calculate_pc_cutoff.R") # source function for determining PC cutoff 
 needed_packages <- c("BiocManager", "dplyr", "knitr", "rmarkdown", "tibble", "ggplot2", 
                      "ggrepel", "broom", "gplots", "tidyr", "sva", "methods")
 installed_packages <- needed_packages %in% rownames(installed.packages())
@@ -95,8 +96,8 @@ if (correction_variable_1 == "PLEASE FILL IN"){
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
   
-  R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-  print(paste0(R, " PCs that explained a minimum of >10% change of variance were included"))
+  R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+  print(paste0(R, " PCs were included"))
   
   phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
     select(personid, plate, slide, array, row, column, arrayid)
@@ -254,8 +255,8 @@ if (correction_variable_2 == "PLEASE FILL IN"){
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
   
-  R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-  print(paste0(R, " PCs that explained a minimum of >10% change of variance were included"))
+  R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+  print(paste0(R, " PCs were included"))
   
   phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
     select(personid, plate, slide, array, row, column, arrayid)
@@ -413,8 +414,8 @@ if (correction_variable_3 == "PLEASE FILL IN"){
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
   
-  R <- variance_explained %>% filter(var_explained > 10) %>% nrow() # threshold for N of PCs
-  print(paste0(R, " PCs that explained >10% change of variance were included"))
+  R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
+  print(paste0(R, " PCs were included"))
   
   phenodata_subset_df <- as.data.frame(PhenoData_clean@listData) %>%
     select(personid, plate, slide, array, row, column, arrayid)