Closed kokyriakidis closed 1 year ago
Hi @kokyriakidis , unfortunately more complex contrasts other than pairwise aren't supported by the R Markdown template, since we're trying to keep it simple for most users.
You can generate the starter DESeqDataSet
with this command:
# Coerce bcbioRNASeq object to DESeqDataset.
dds <- as.DESeqDataSet(bcb)
Then follow the recommendations in the DESeq2 vignette.
In this part:
deseq <- DESeqAnalysis(
data = dds,
transform = dt,
results = resListUnshrunken,
lfcShrink = resListShrunken
)
saveData(deseq, dir = params[["data_dir"]])
I get an error:
Error in validObject(.Object) :
invalid class "DESeqAnalysis" object: DESeqResults list must be named.
If supported, 'updateObject' may help resolve these issues.
I should change resListUnshrunken to resListUnshrunken[[1]] or something like that to select the contrast I want. Is there a easier way to automatically do it for all contrasts?
Just ensure that resListUnshrunken
and resListShrunken
are named, with matching names -- i.e. what is the name of the contrast you ran? This is a sanity check in the DESeqAnalysis
object to ensure there is sufficient metadata for the current analysis.
Hi @kokyriakidis , I'm going to close this issue because it's outside the scope of the bcbioRNASeq package. Let me know if this would still be useful, and I can think about adding support for complex interactions in DESeqAnalysis.
Hi @mjsteinbaugh !
I have a quick question:
Let's say I want to make the following interactions:
That's easy on the template.
What if I wanted to test the interaction of interactions? Does that make sense? How do I do that in the contrasts?