Bioconductor YAPSA

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YAPSA

updated 2.7 years ago by Marc • 0 • written 5.7 years ago by TRASA • 0

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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: How to visualize these pathways using pathview by ingrid.h • 0

Yes I have seen it, thanks.

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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Comment: Weird p-values using DESeq2?

Answer: Store Matrix in DataFrame Cell

Answer: enrichGOgradient color change

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