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  3. Differential Expression Analysis with limma in R

Exercise

Remove batch effects

In the previous exercise, you demonstrated that the effect of batch had a larger impact on the variation compared to the effect of treatment. Fortunately, the olfactory stem cell study was perfectly balanced, i.e. each treatment was included in all 4 of the batches. Thus you can remove the variation introduced by the batch processing to increase the signal-to-noise ratio.

Instructions

100 XP

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

  • Use removeBatchEffect to remove the effect of the 4 batches from the data.
  • Use plotMDS to plot the principal components. Label the samples by the treatment they received.
  • Re-visualize the principal components, labeling the samples by their batch.