DE解析の概要

RNA-Seq with Bioconductor in R

Mary Piper

Bioinformatics Consultant and Trainer

データセット／研究課題の確認

fibrosis_experiment

RNA-Seq with Bioconductor in R

DE解析の概要

DESeq2ワークフロー

RNA-Seq with Bioconductor in R

DESeq2ワークフロー - モデル

RNA-Seq with Bioconductor in R

DESeq2ワークフロー：モデル

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

deseqオブジェクト

RNA-Seq with Bioconductor in R

DESeq2ワークフロー：デザイン式

example_metadata

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

DESeq2ワークフロー：デザイン式

example_metadata

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

DESeq2ワークフロー：実行

# 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オブジェクト

RNA-Seq with Bioconductor in R

練習しましょう！

RNA-Seq with Bioconductor in R

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