From bade2831982fa26eee0b28822a5495574642b700 Mon Sep 17 00:00:00 2001 From: Viktoria Petrova <vipet103@hhu.de> Date: Sat, 5 Oct 2024 15:19:55 +0200 Subject: [PATCH] add differential expression analysis assay and protocol --- assays/DifferentialExpressionAnalysis/README.md | 0 .../dataset/.gitkeep | 0 .../isa.assay.xlsx | Bin 0 -> 6907 bytes .../protocols/.gitkeep | 0 .../DifferentialGeneExpressionAnalysis.md | 3 +++ 5 files changed, 3 insertions(+) create mode 100644 assays/DifferentialExpressionAnalysis/README.md create mode 100644 assays/DifferentialExpressionAnalysis/dataset/.gitkeep create mode 100644 assays/DifferentialExpressionAnalysis/isa.assay.xlsx create mode 100644 assays/DifferentialExpressionAnalysis/protocols/.gitkeep create mode 100644 assays/DifferentialExpressionAnalysis/protocols/DifferentialGeneExpressionAnalysis.md diff --git a/assays/DifferentialExpressionAnalysis/README.md b/assays/DifferentialExpressionAnalysis/README.md new file mode 100644 index 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b/assays/DifferentialExpressionAnalysis/protocols/DifferentialGeneExpressionAnalysis.md @@ -0,0 +1,3 @@ +## Differential expression analysis + +Differentially expressed genes between microbe treatments and mock treatments were identified using Sleuth (Pimentel et al., 2017; Figure S2). The p-values were adjusted using the Benjamini-Hochberg correction (FDR ≤ 0.05; Benjamini and Hochberg, 1995). Since Sleuth relies on replicates within treatments, BioProjects without replicates were removed from this part of analysis. We evaluated differences between i) *R*-genes and all genes, ii) proportion of up- versus down-regulation iii) average absolute fold changes \ No newline at end of file -- GitLab