Přehled DE analýzy

RNA-Seq s Bioconductorem v R

Mary Piper

Bioinformatics Consultant and Trainer

Přehled datové sady a otázky

fibrosis_experiment

RNA-Seq s Bioconductorem v R

Přehled DE analýzy

Workflow DESeq2

RNA-Seq s Bioconductorem v R

Workflow DESeq2 – model

RNA-Seq s Bioconductorem v R

Workflow DESeq2: Model

# Create DESeq object 
dds_wt <- DESeqDataSetFromMatrix(countData = wt_rawcounts,
                              colData = reordered_wt_metadata,
                              design = ~ condition)

Objekt DESeq

RNA-Seq s Bioconductorem v R

Workflow DESeq2: Designový vzorec

example_metadata

# Design formula 
~ strain + sex + treatment
RNA-Seq s Bioconductorem v R

Workflow DESeq2: Designový vzorec

example_metadata

# Design formula 
~ strain + sex + treatment + sex:treatment
RNA-Seq s Bioconductorem v R

Workflow DESeq2: Spuštění

# Run analysis
dds_wt <- DESeq(dds_wt)

using pre-existing size factors
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing

Objekt DESeq

RNA-Seq s Bioconductorem v R

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RNA-Seq s Bioconductorem v R

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