From 5f7b9a35d9d405104a6a439bab84578e67947f71 Mon Sep 17 00:00:00 2001 From: "Vera N. Karlbauer" Date: Tue, 13 Aug 2024 16:28:55 +0200 Subject: [PATCH] Updated script description for more clarity. --- scripts/3_quality_control.Rmd | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/scripts/3_quality_control.Rmd b/scripts/3_quality_control.Rmd index 2480c74..8ef3db5 100644 --- 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.
**Notes:**