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Comment: Weird p-values using DESeq2?
by
ATpoint
★
4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `ntd()` or `vst/…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★
13k
Dear Ingrid,
thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Comment: Store Matrix in DataFrame Cell
by
Dario Strbenac
★
1.6k
It does not appear to work.
> DataFrame(name = "test", value = list(matrix(1:4, ncol = 2)))
DataFrame with 2 rows and 3 columns
…
Comment: Overcoming confounding in batch effect correction
by
Dario Strbenac
★
1.6k
Actually, it is directly related. ComBat-seq is a part of [sva][1] package. It should use sva tag.
[1]: https://bioconductor.org/package…
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