DESeq2 model – kontrasty

RNA-Seq s Bioconductorem v R

Mary Piper

Bioinformatics Consultant and Trainer

Workflow DESeq2

Workflow DESeq2 – zmenšení LFC

RNA-Seq s Bioconductorem v R

Workflow DESeq2

# 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 s Bioconductorem v R

DESeq2 – negativně binomický model

Model NB

RNA-Seq s Bioconductorem v R

DESeq2 – negativně binomický model

Model NB2

RNA-Seq s Bioconductorem v R

DESeq2 kontrasty

results(wt_dds, alpha = 0.05)

výstup kontrastu

RNA-Seq s Bioconductorem v R

DESeq2 kontrasty

Syntaxe je:

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 s Bioconductorem v R

DESeq2 kontrasty

wt_res

výstup kontrastu

RNA-Seq s Bioconductorem v R

DESeq2 – zmenšení LFC

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

MA plot – neshrnuté fold changes

RNA-Seq s Bioconductorem v R

Zmenšení LFC

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

plotMA(wt_res, ylim=c(-8,8))
RNA-Seq s Bioconductorem v R

Zmenšení LFC

MA plot – shrnuté fold changes

RNA-Seq s Bioconductorem v R

Pojďme procvičovat!

RNA-Seq s Bioconductorem v R

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