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Comment: Extract LRT results for each comparison
by
ATpoint
★
3.4k
If you want to contrast the timepoints then the latter contrast is valid. The influence of `orig.ident` has already been taken care of as p…
Answer: Biostrings error at retrieving protein sequences
by
James W. MacDonald
63k
You appear to have already answered your question. But to confirm, computers are dumb and will not match two things that aren't exactly ide…
Answer: Biostrings error at retrieving protein sequences
by
ATpoint
★
3.4k
Yes, this error comes up when you try to subset with names that do not exist in the AAStringSet, for example:
```r
library(Biostrings)
…
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 …
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