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  3. RNA-Seq with Bioconductor in R

Exercise

DE analysis

NOTE: It may take a bit longer to load this exercise.

We are going to continue using the full dataset comparing the genes that exhibit significant expression differences between normal and fibrosis samples regardless of genotype (design: ~ genotype + condition). Therefore, we will use our dds_all DESeq2 object created in the previous exercise. Assume this object is created and all libraries are loaded. In this exercise let's perform the unsupervised clustering analyses to explore the clustering of our samples and sources of variation.

Instructions

100 XP

  • Log transform the normalized counts inside the dds_all object using the vst() function, being blind to sample group information.

  • Create the correlation heatmap of the correlation values of the log normalized counts using the pheatmap() function. Include annotation bars for genotype and condition.

  • Plot the PCA with the plotPCA() function using vsd_all. Color the plot by condition.

  • Plot the PCA with the plotPCA() function using vsd_all. Color the plot by genotype.