From 4d1fa2cc1fd32ff157e51e236098d15f2ecd1440 Mon Sep 17 00:00:00 2001 From: Mia Pras-Raves Date: Thu, 2 Apr 2026 09:29:57 +0200 Subject: [PATCH 1/2] fixed bug in filtered replication_pattern in DIMS/EvaluateTICs.R --- DIMS/EvaluateTics.R | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/DIMS/EvaluateTics.R b/DIMS/EvaluateTics.R index 37e672a..521430e 100644 --- a/DIMS/EvaluateTics.R +++ b/DIMS/EvaluateTics.R @@ -44,15 +44,17 @@ print(remove_tech_reps) remove_neg <- remove_tech_reps$neg repl_pattern_filtered <- remove_from_repl_pattern(remove_neg, repl_pattern, nr_replicates) save(repl_pattern_filtered, file = "negative_repl_pattern.RData") +# get an overview of suitable technical replicates for both negative mode +allsamples_techreps_neg <- get_overview_tech_reps(repl_pattern_filtered, "negative") # positive scan mode remove_pos <- remove_tech_reps$pos repl_pattern_filtered <- remove_from_repl_pattern(remove_pos, repl_pattern, nr_replicates) save(repl_pattern_filtered, file = "positive_repl_pattern.RData") - -# get an overview of suitable technical replicates for both scan modes -allsamples_techreps_neg <- get_overview_tech_reps(repl_pattern_filtered, "negative") +# get an overview of suitable technical replicates for positive scan mode allsamples_techreps_pos <- get_overview_tech_reps(repl_pattern_filtered, "positive") + +# get an overview of suitable technical replicates for both scan modes and save to file allsamples_techreps_both_scanmodes <- rbind(allsamples_techreps_pos, allsamples_techreps_neg) write.table(allsamples_techreps_both_scanmodes, file = "replicates_per_sample.txt", From 48cc0dab38cb539da5167b146b05b712385b28fb Mon Sep 17 00:00:00 2001 From: Mia Pras-Raves Date: Tue, 7 Apr 2026 15:21:47 +0200 Subject: [PATCH 2/2] fixed bug in internal standard table in DIMS/GenerateQCOutput --- DIMS/GenerateQCOutput.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DIMS/GenerateQCOutput.R b/DIMS/GenerateQCOutput.R index 2efb4d5..d22c337 100644 --- a/DIMS/GenerateQCOutput.R +++ b/DIMS/GenerateQCOutput.R @@ -208,7 +208,7 @@ if (dims_matrix == "Plasma") { } if (nrow(is_below_threshold) > 0) { - write.table(cbind(is_below_threshold, scanmode = scanmode_is), + write.table(is_below_threshold, file = "internal_standards_below_threshold.txt", row.names = FALSE, sep = "\t") } else {