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
Exercise instructions
- Use the
results()
function to specify the contrast for the comparison using an alpha of0.05
. For the condition of interest,condition
, output the results for thefibrosis
sample group relative to thenormal
sample group, so that thenormal
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 = ___)