The two datasets GSE3585 and GSE5406 were loaded onto the GPL96 platform (Affymetrix Human Genome U133A Array [HG-U133A]). Additionally, the series matrix and platform annotation for the two databases were downloaded from the GEO database. The probe identity documents were transformed into gene symbols. Then, via the R package “Surrogate Variable Analysis,” the two databases were merged, and any batch effect was removed using the “Empirical Bayes” method[21 (link)]. The R package “limma” was applied to identify the DEGs between the DCM and healthy myocardium tissues[22 (link)]. The screening criteria were set as P < 0.05 and |log fold change (FC)| > 0.589 (FC > 1.5). Volcano and heat maps were generated using R software.
Protocol detail
Differential Gene Expression Analysis of DCM
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Gene
Human genome
Maps
Myocardium tissues
Corresponding Organization :
Other organizations : Guiyang Medical University
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Variable analysis
independent variables
- Healthy myocardium
- Differentially Expressed Genes (DEGs)
- GPL96 platform (Affymetrix Human Genome U133A Array [HG-U133A])
- Empirical Bayes method for batch effect removal
- Screening criteria: P < 0.05 and |log fold change (FC)| > 0.589 (FC > 1.5)
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