Bioconductor LC-MS/MS

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msnbase msmstests proteomics lc-ms/ms msnID

updated 6.0 years ago by Laurent Gatto 1.6k • written 6.0 years ago by fgol ▴ 10

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XCMS LC-MS LC-MS/MS Alignment

updated 4.8 years ago by Johannes Rainer ★ 2.1k • written 4.8 years ago by ljveillon • 0

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proteomics LC-MS/MS

updated 5.9 years ago by Laurent Gatto 1.6k • written 5.9 years ago by pdaltron • 0

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Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k

> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…

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 `normTransform()…

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 …

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