DESeq2 model - contrasts

RNA-Seq with Bioconductor in R

Mary Piper

Bioinformatics Consultant and Trainer

DESEq2 workflow

DESeq2 workflow - LFC shrinkage

RNA-Seq with Bioconductor in R

DESeq2 workflow

# 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
RNA-Seq with Bioconductor in R

DESeq2 Negative Binomial Model

NB model

RNA-Seq with Bioconductor in R

DESeq2 Negative Binomial Model

NB model2

RNA-Seq with Bioconductor in R

DESeq2 contrasts

results(wt_dds, alpha = 0.05)

contrast output

RNA-Seq with Bioconductor in R

DESeq2 contrasts

The syntax is:

results(dds, 
        contrast = c("condition_factor", "level_to_compare", 
        "base_level"), 
        alpha = 0.05)

wt_res <- results(dds_wt, 
            contrast = c("condition", "fibrosis", 
            "normal"), 
            alpha = 0.05)
RNA-Seq with Bioconductor in R

DESeq2 contrasts

wt_res

contrast output

RNA-Seq with Bioconductor in R

DESeq2 LFC shrinkage

plotMA(wt_res, ylim=c(-8,8))

MA plot unshrunken foldchanges

RNA-Seq with Bioconductor in R

LFC shrinkage

wt_res <- lfcShrink(dds_wt, 
            contrast=c("condition", "fibrosis", "normal"),
            res=wt_res)

plotMA(wt_res, ylim=c(-8,8))
RNA-Seq with Bioconductor in R

LFC shrinkage

MA plot shrunken foldchanges

RNA-Seq with Bioconductor in R

Let's practice!

RNA-Seq with Bioconductor in R

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