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Answer: Extract LRT results for each comparison
by
James W. MacDonald
63k
Your first test is asking if you need to include orig.ident in the model at all. It doesn't test *anything* about the timepoints. If you wa…
Comment: Interpretation of LRT results
by
James W. MacDonald
63k
You need to pay attention to the output.
```
> dds <- makeExampleDESeqDataSet()
> colData(dds)$condition <- factor(rep(LETTERS[1:3], each …
Comment: Extract LRT results for each comparison
by
Yijing
•
0
Thank you for your quick reply!
In the contrast tutorial, the example is `results(dds, contrast=c("condition","C","B"))`. In my case, I al…
Comment: bug in block.plsda from mixOmics?
by
James W. MacDonald
63k
But `block.plsda` calls `internal_wrapper.mint.block` with DA = TRUE, so the default doesn't matter. You'll need to provide the output from…
Answer: Extract LRT results for each comparison
by
ATpoint
★
3.4k
1) The design does not impact the PCA. If you want to see effects on adding or removing design covariates then you have to regress the cova…
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