Updated script description for more clarity.

mpip · Aug 13, 2024 · 5f7b9a3 · 5f7b9a3
1 parent 5d02e93
commit 5f7b9a3
Showing 1 changed file with 5 additions and 3 deletions.
diff --git a/scripts/3_quality_control.Rmd b/scripts/3_quality_control.Rmd
@@ -42,11 +42,13 @@ summary_table_preprocessing <- readRDS(paste0(user_choices$project_name, "/repor
 
 This script  
 
-* removes samples with detection *p* values lower that threshold set by user (default 0.05)  
-* saves person IDs of failed samples  
+* calculates detection *p* values for each probe and sample  
+* removes samples with detection *p* values higher that threshold set by user (default 0.05)  
+* saves person IDs of failed samples (with insufficient detection *p* values)  
 * generates reports of poor quality samples according to detection *p* values  
 * generates minfi QC report for remaining samples  
-* generates Individual Density report, asks user to visually examine.  
+* generates Individual Density report, asks user to visually examine  
+Please note: Probes with high detection *p* values are not yet removed in this step, but in script 6.  
 
 <br>  
 **Notes:**