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DESeq2 results - LFC shrinkage

NOTE: It may take a bit longer to load this exercise.

To improve the fold change estimates for our data, we want to take our results and shrink the log2 fold changes using the lfcShrink() function.

Assume all prior steps have been executed, including the creation of the DESeq2 object, dds_smoc2, running the DESeq() function, and extracting the results, smoc2_res.

This exercise is part of the course

RNA-Seq with Bioconductor in R

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Exercise instructions

  • Perform shrinkage of the log2 foldchanges using the lfcShrink() function.

Hands-on interactive exercise

Have a go at this exercise by completing this sample code.

# Shrink the log2 fold change estimates to be more accurate
smoc2_res <- lfcShrink(___, 
                    contrast =  c(___, ___, ___),
                    res = ___)
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