Overview of the DE analysis

RNA-Seq with Bioconductor in R

Mary Piper

Bioinformatics Consultant and Trainer

Review the dataset/question

fibrosis_experiment

RNA-Seq with Bioconductor in R

Overview of the DE analysis

DESeq2 workflow

RNA-Seq with Bioconductor in R

DESeq2 workflow - model

RNA-Seq with Bioconductor in R

DESeq2 workflow: Model

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

deseq object

RNA-Seq with Bioconductor in R

DESeq2 workflow: Design formula

example_metadata

# Design formula 
~ strain + sex + treatment
RNA-Seq with Bioconductor in R

DESeq2 workflow: Design formula

example_metadata

# Design formula 
~ strain + sex + treatment + sex:treatment
RNA-Seq with Bioconductor in R

DESeq2 workflow: Running

# 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

DESeq object

RNA-Seq with Bioconductor in R

Let's practice!

RNA-Seq with Bioconductor in R

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