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)?
Deze oefening maakt deel uit van de cursus
Differential Expression Analysis with limma in R
Oefeninstructies
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.
Praktische interactieve oefening
Probeer deze oefening eens door deze voorbeeldcode in te vullen.
# Plot principal components labeled by genotype
___(eset, labels = ___(eset)[___], gene.selection = "common")
# Plot principal components labeled by treatment
___(eset, labels = ___(eset)[___], gene.selection = "common")