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DESeq2 model - extracting results

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

After exploring the dispersions and deciding the data fits the DESeq2 model well, we want to extract the results.

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

This exercise is part of the course

RNA-Seq with Bioconductor in R

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Exercise instructions

  • Use the results() function to specify the contrast for the comparison using an alpha of 0.05. For the condition of interest, condition, output the results for the fibrosis sample group relative to the normal sample group, so that the normal sample group is the base level.

Hands-on interactive exercise

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

# Extract the results of the differential expression analysis
smoc2_res <- results(___, 
                ___ = ___, 
                alpha = ___)
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