Check sources of variation
Next you need to use principal components analysis to check for the sources of variation in the data. Do the samples cluster by their genotype (WT vs. Top2b null) and treatment (PBS vs. Dox)?
This exercise is part of the course
Differential Expression Analysis with limma in R
Exercise instructions
The ExpressionSet object eset with the doxorubicin data has been loaded in your workspace. The limma package is already loaded.
Use
plotMDSto plot the principal components. Label the samples by their genotype.Re-visualize the principal components, labeling the samples by their treatment.
Hands-on interactive exercise
Have a go at this exercise by completing this sample code.
# Plot principal components labeled by genotype
___(eset, labels = ___(eset)[___], gene.selection = "common")
# Plot principal components labeled by treatment
___(eset, labels = ___(eset)[___], gene.selection = "common")