Corrected name of unfiltered annotation

mpip · Aug 14, 2024 · 9ff8c73 · 9ff8c73
1 parent 7230a8b
commit 9ff8c73
Showing 1 changed file with 2 additions and 2 deletions.
diff --git 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"