diff --git a/scripts/9_correction_batch_effects_filtered.Rmd b/scripts/9_correction_batch_effects_filtered.Rmd
index 17500de..777c58d 100644
--- a/scripts/9_correction_batch_effects_filtered.Rmd
+++ b/scripts/9_correction_batch_effects_filtered.Rmd
@@ -97,7 +97,7 @@ if (correction_variable_1 == "PLEASE FILL IN"){
                                    var_explained = 100*round(summary(PCA_object)$importance[2,], 2),
                                    cumm_var_explained = 100*round(summary(PCA_object)$importance[3,], 2))
   
-  variance_explained %>%
+screeplot <- variance_explained %>%
     dplyr::slice(1:10) %>%
     ggplot(aes(x = factor(PC, level = PC), y = var_explained, group = 1)) +
     geom_point() +
@@ -105,6 +105,7 @@ if (correction_variable_1 == "PLEASE FILL IN"){
     geom_text(aes(label = cumm_var_explained), vjust = 1.5) +
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
+print(screeplot)
   
   R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
   print(paste0(R, " PCs were included"))
@@ -241,7 +242,8 @@ if (correction_variable_1 == "PLEASE FILL IN"){
 ```
 
 ```{r, print p-value table for batch effects after correction of first batch effect variable}
-anova_lm_pvalue_df %>% paged_table()
+if (correction_variable_1 != "PLEASE FILL IN"){
+  anova_lm_pvalue_df %>% paged_table()}
 ```
 
 ```{r, correction of second batch effect and PCA, results='asis'}
@@ -260,7 +262,7 @@ if (correction_variable_2 == "PLEASE FILL IN"){
                                    var_explained = 100*round(summary(PCA_object)$importance[2,], 2),
                                    cumm_var_explained = 100*round(summary(PCA_object)$importance[3,], 2))
   
-  variance_explained %>%
+screeplot <-  variance_explained %>%
     dplyr::slice(1:10) %>%
     ggplot(aes(x = factor(PC, level = PC), y = var_explained, group = 1)) +
     geom_point() +
@@ -268,6 +270,7 @@ if (correction_variable_2 == "PLEASE FILL IN"){
     geom_text(aes(label = cumm_var_explained), vjust = 1.5) +
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
+print(screeplot)
   
   R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
   print(paste0(R, " PCs were included"))
@@ -404,7 +407,8 @@ if (correction_variable_2 == "PLEASE FILL IN"){
 ```
 
 ```{r, print p-value table for batch effects after correction of second batch effect variable}
-anova_lm_pvalue_df %>% paged_table()
+if (correction_variable_2 == "PLEASE FILL IN"){
+  anova_lm_pvalue_df %>% paged_table()}
 ```
 
 ```{r, correction of third batch effect and PCA}
@@ -423,7 +427,7 @@ if (correction_variable_3 == "PLEASE FILL IN"){
                                    var_explained = 100*round(summary(PCA_object)$importance[2,], 2),
                                    cumm_var_explained = 100*round(summary(PCA_object)$importance[3,], 2))
   
-  variance_explained %>%
+screeplot <- variance_explained %>%
     dplyr::slice(1:10) %>%
     ggplot(aes(x = factor(PC, level = PC), y = var_explained, group = 1)) +
     geom_point() +
@@ -431,6 +435,7 @@ if (correction_variable_3 == "PLEASE FILL IN"){
     geom_text(aes(label = cumm_var_explained), vjust = 1.5) +
     labs(x = "Principal Component", y = "Variance Explained (%)", title = "Scree Plot",
          subtitle = "Note: cumulative variance explained (%) is displayed as text")
+print(screeplot)
   
   R <- pc_cutoff(variance_explained) # automatically calculate number of PCs
   print(paste0(R, " PCs were included"))
@@ -566,7 +571,8 @@ if (correction_variable_3 == "PLEASE FILL IN"){
 ```
 
 ```{r, print p-value table for batch effects after correction of third batch effect variable}
-anova_lm_pvalue_df %>% paged_table()
+if (correction_variable_3 == "PLEASE FILL IN"){
+  anova_lm_pvalue_df %>% paged_table()}
 ```
 
 ```{r, convertion M to Beta and save, include=FALSE}