From 9ff8c73e8443364b47e141bd631008166725c24e Mon Sep 17 00:00:00 2001 From: "Vera N. Karlbauer" Date: Wed, 14 Aug 2024 13:01:28 +0200 Subject: [PATCH] Corrected name of unfiltered annotation --- scripts/7_normalization.Rmd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/7_normalization.Rmd b/scripts/7_normalization.Rmd index a8e8adc..f9e8abf 100644 --- a/scripts/7_normalization.Rmd +++ b/scripts/7_normalization.Rmd @@ -48,7 +48,7 @@ load(paste0(user_choices$project_name, "/processed_data/Betas_clean_filtered.Rda load(paste0(user_choices$project_name, "/processed_data/PhenoData_clean.Rdata")) load(paste0(user_choices$project_name, "/processed_data/RGSet_clean.Rdata")) load(paste0(user_choices$project_name, "/processed_data/Betas_clean.Rdata")) -load(paste0(user_choices$project_name, "/reports/annotations_clean.Rdata")) +load(paste0(user_choices$project_name, "/reports/annotations_clean_unfiltered.Rdata")) load(paste0(user_choices$project_name, "/reports/annotations_clean_filtered.Rdata")) ``` @@ -115,7 +115,7 @@ Ms_clean_unfiltered_qunatile <- getM(gRatioSet_clean_unfiltered_quantile) save(Ms_clean_unfiltered_qunatile, file = paste0(user_choices$project_name, "/processed_data/Ms_clean_unfiltered_qunatile.Rdata")) # further normalization with BMIQ: -probeType <- as.data.frame(annotations_clean[rownames(Betas_clean_unfiltered_quantile),c("Name","Type")]) +probeType <- as.data.frame(annotations_clean_unfiltered[rownames(Betas_clean_unfiltered_quantile),c("Name","Type")]) probeType$probeType = ifelse(probeType$Type %in% "I", 1, 2) Betas_clean_unfiltered_quantile_bmiq <- apply(Betas_clean_unfiltered_quantile[,1:length(colnames(Betas_clean_unfiltered_quantile))],2, function(a) BMIQ(a,probeType$probeType,plots=FALSE)$nbeta) # sourced from script "BMIQ_1.6_Teschendorff.R"