Exercises: Clustering and heatmaps

Go to parent Introduction to R/Bioconductor for analysis of microarray data#Training Units

Grouping primates

The package fibroEset contains gene expression data for fibrobalst cell lines from 18 human, 10 bonobo and 11 gorilla donors. Select the 300 genes with the largest variability (as measured by the interquartile range) and produce a cluster heatmap that shows how the species are arranged based on their expression data.

Pathway clustering

A recent publication by Crespo-Barreto et al. has found a number of KEGG pathways to be regulated between Ataxin1 KO and WT mice (PubMed ID 20628574, Table S2). Pick the three top-regulated pathways and visualize their expression in our data set, using the function KEGG2heatmap in package annotate. link to PMC

Example commands on heatmap