Unsupervised clustering analyses

RNA-Seq with Bioconductor in R

Mary Piper

Instructor

DESeq2 worflow - QC

RNA-Seq with Bioconductor in R

Unsupervised clustering analyses: log transformation

vsd_wt <- vst(dds_wt, blind=TRUE)
RNA-Seq with Bioconductor in R

heatmap example

RNA-Seq with Bioconductor in R

Hierarchical clustering with correlation heatmaps

# Extract the vst matrix from the object
vsd_mat_wt <- assay(vsd_wt) 
# Compute pairwise correlation values
vsd_cor_wt <- cor(vsd_mat_wt) 
View(vsd_cor_wt)

correlation matrix

RNA-Seq with Bioconductor in R

Hierarchical clustering with correlation heatmaps

# Load pheatmap libraries
library(pheatmap) 

# Plot heatmap
pheatmap(vsd_cor_wt, annotation = select(wt_metadata, condition))
RNA-Seq with Bioconductor in R

Hierarchical clustering with correlation heatmaps

wildtype heatmap

RNA-Seq with Bioconductor in R

Let's practice!

RNA-Seq with Bioconductor in R

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