DESeq2 results exploration
NOTE: It may take a bit longer to load this exercise.
To reduce the number of DE genes that we are returning and to reduce the likelihood of the DE genes being biologically meaningful, we are going to use a small log2 fold change threshold to determine the DE genes.
This exercise is part of the course
RNA-Seq with Bioconductor in R
Exercise instructions
Extract the smoc2 results using the
results()
function, similar to before, with an alpha of 0.05 and withnormal
as the base level ofcondition
. However, this time use a log2 fold change threshold of 0.32. Assume all prior steps have been executed, including the creation of the DESeq2 object,dds_smoc2
, and running theDESeq()
function.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.
# Explore the results() function
?results
# Extract results
smoc2_res <- ___(___,
contrast = ___,
alpha = ___,
lfcThreshold = ___)
# Shrink the log2 fold changes
smoc2_res <- ___(___,
___,
res = ___)