What comes first: count normalization or gene/sample filtering?
Normalization
Filtering
Trimmed Mean of M values
Lowly-expressed genes
Low-quality samples
RNA-seq
Trimmed Mean of M-values
Normalization
RNA composition bias
Trimmed Mean of M-values
Library size
Normalization factor
Highly-expressed genes
Differential Gene Expression
RNA-seq
Understading coefficients in linear models fits for RNA-seq data
coefficient
beta
interaction terms
contrast
multi-level variable
Fisher's exact test for enrichment analysis of gene sets
Fisher's exact test
overrepresentation
ORA
enrichment
Gene Set Enrichment Analysis
GO
KEGG
Functional enrichment
MAGMA: How does the Gene and the Gene-Set analysis operate?
GWAS
Gene Analysis
Gene Set Analysis
SNP summary statistics
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