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.