From 33541176f88627d8a4884182434be61006c592cd Mon Sep 17 00:00:00 2001 From: jfallmann Date: Wed, 1 Apr 2026 15:50:13 +0200 Subject: [PATCH] edger cleanup --- scripts/Analysis/DAS/EDGER.R | 3 +-- scripts/Analysis/DE/EDGER.R | 4 +--- scripts/Analysis/DEU/EDGER.R | 3 +-- 3 files changed, 3 insertions(+), 7 deletions(-) diff --git a/scripts/Analysis/DAS/EDGER.R b/scripts/Analysis/DAS/EDGER.R index ff19817e..f38a7c21 100755 --- a/scripts/Analysis/DAS/EDGER.R +++ b/scripts/Analysis/DAS/EDGER.R @@ -245,8 +245,7 @@ for (compare in comparisons[[1]]) { # } # contrast <- as.numeric(contrast[,1]) - # create files topSpliced by gene, simes and exon method - # sp <- diffSpliceDGE(fit, contrast=contrast, geneid="genes", exonid="exons", verbose=FALSE) + # create files topSpliced by gene, simes and exon method sp <- diffSpliceDGE(fit, geneid = "genes", exonid = "exons", verbose = FALSE) # add comp object to list for image diff --git a/scripts/Analysis/DE/EDGER.R b/scripts/Analysis/DE/EDGER.R index 38f563a2..6ed8bcfb 100755 --- a/scripts/Analysis/DE/EDGER.R +++ b/scripts/Analysis/DE/EDGER.R @@ -318,9 +318,7 @@ for (contrast in comparison[[1]]) { # contrast[which(contrast[,2]==i)]<- plus # } # contrast <- as.numeric(contrast[,1]) - - ## Testing - # qlf <- glmQLFTest(fit, contrast=contrast) ## glm quasi-likelihood-F-Test + AvsB <- makeContrasts(TreatvsUntreat = paste("condition", A, sep = ""), levels = design) qlf <- glmQLFTest(fit, contrast = AvsB) ## glm quasi-likelihood-F-Test # add comp object to list for image diff --git a/scripts/Analysis/DEU/EDGER.R b/scripts/Analysis/DEU/EDGER.R index 72468280..763a4afa 100755 --- a/scripts/Analysis/DEU/EDGER.R +++ b/scripts/Analysis/DEU/EDGER.R @@ -239,8 +239,7 @@ for (compare in comparisons[[1]]) { # } # contrast <- as.numeric(contrast[,1]) - # quasi-likelihood F-Test - # qlf <- glmQLFTest(fit, contrast = contrast) + # quasi-likelihood F-Test qlf <- glmQLFTest(fit) is.de <- decideTests(qlf, p.value = 0.05)