From 55540b4f72db09b0a054b03a207ea93a8cb3169a Mon Sep 17 00:00:00 2001 From: Natan Yusupov Date: Thu, 12 Oct 2023 13:32:15 +0200 Subject: [PATCH] type fixes README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 342b38e..700b172 100644 --- a/README.md +++ b/README.md @@ -30,7 +30,7 @@ The workflow contains a variety of steps, including quality control, CpG filteri **Quality Control**
-The workflow will find and remove low quality or unreliable samples from the data. The pipeline does this by calculating detection p-values (detP), which indicate the quality. ***minifi***, the R package used in this pipeline, creates the detP values by comparing the total signal of unmethylated and methuylated (M+U) for each CpG to a background signal level, approximated from negative control probes. A small p-value indicates reliable signal while large p-values indicate poor quality signals. We also provide the minfi qcreport, which generates other quality control plots. Poor samples are then excluded from further processing and analysis by using a detP cutoff value set by the user. +The workflow will find and remove low quality or unreliable samples from the data. The pipeline does this by calculating detection p-values (detP), which indicate the quality. ***minfi***, the R package used in this pipeline, creates the detP values by comparing the total signal of unmethylated and methuylated (M+U) for each CpG to a background signal level, approximated from negative control probes. A small p-value indicates reliable signal while large p-values indicate poor quality signals. We also provide the minfi qcreport, which generates other quality control plots. Poor samples are then excluded from further processing and analysis by using a detP cutoff value set by the user.
**Calculating M and beta values**