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  3. Differential Expression Analysis with limma in R

Exercise

Visualize batch effects

In the olfactory stem cell experiment, there were 7 treatments with 4 replicates each for a total of 28 samples. However, these 28 samples were processed in 4 separate batches. The effect of the treatments is of biological interest, but the effect of the batches is technical noise. Using dimension reduction, determine which of these two effects had a larger impact on the gene expression data.

Instructions

100 XP

The ExpressionSet object eset with the olfactory stem cell data has been loaded in your workspace.

  • Use plotMDS to plot the principal components. Label the samples by the treatment they received, and set gene.selection to "common".

  • Re-visualize the principal components, labeling the samples by their batch.