From 2ffcd20c6466391bb021e3f97ae8647de9a53cca Mon Sep 17 00:00:00 2001
From: Viktoria Petrova <vipet103@hhu.de>
Date: Sun, 10 Nov 2024 12:18:27 +0100
Subject: [PATCH] add ANOVA analysis assay and protocol
---
.../README.md | 0
.../dataset/.gitkeep | 0
.../isa.assay.xlsx | Bin 0 -> 6917 bytes
.../protocols/.gitkeep | 0
...ifferentialEnrichmentOfMetabolitesProtocol.md | 3 +++
5 files changed, 3 insertions(+)
create mode 100644 assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md
create mode 100644 assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/.gitkeep
create mode 100644 assays/ANOVAForDifferentialEnrichmentOfMetabolites/isa.assay.xlsx
create mode 100644 assays/ANOVAForDifferentialEnrichmentOfMetabolites/protocols/.gitkeep
create mode 100644 assays/ANOVAForDifferentialEnrichmentOfMetabolites/protocols/ANOVAForDifferentialEnrichmentOfMetabolitesProtocol.md
diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/README.md
new file mode 100644
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diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/.gitkeep b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/dataset/.gitkeep
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diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/isa.assay.xlsx b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/isa.assay.xlsx
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diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/protocols/.gitkeep b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/protocols/.gitkeep
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diff --git a/assays/ANOVAForDifferentialEnrichmentOfMetabolites/protocols/ANOVAForDifferentialEnrichmentOfMetabolitesProtocol.md b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/protocols/ANOVAForDifferentialEnrichmentOfMetabolitesProtocol.md
new file mode 100644
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+++ b/assays/ANOVAForDifferentialEnrichmentOfMetabolites/protocols/ANOVAForDifferentialEnrichmentOfMetabolitesProtocol.md
@@ -0,0 +1,3 @@
+## ANOVA for differential enrichment of metabolites
+
+We applied the python package *statsmodels* (Seabold, S. and Perktold, J., 2010) to perform two-way analysis of variance (ANOVA) (Girden, E., 1992). For a particular metabolite, we collected its mass spectrometry relative response in the WT or in sweet knockouts (line: WT vs. SWEET), and at different segments of the root (region: 2cm vs. 4cm vs. 6cm vs. whole). We fit a model that decomposes the relative response of the metabolite as a combination of line-specific and region-specific factors; this model is described by the following string in the code: *‘relativeResponse ∼ Line + Region'* and calculates a *P*-value for *Line* and one for *Region*. Using the *P*-value cutoff of 0.05 for *Line* (and *Region*), we determined the relative response of the metabolite to change significantly with *Line* (*Region*) if *P* <0.05.
\ No newline at end of file
--
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