Question

Calculating the contrast of two genotypes "vs"

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Wuschel ▴ 10

@wuschel-15944

Last seen 14 months ago

HUJI

I came across this new "Mass Spectrometry Downstream Analysis Pipeline (MS-DAP)" R package. It uses 'ProtGenerics', 'MSnbase', 'limma' Bioconductor packages. https://github.com/ftwkoopmans/msdap

In its example, contrast is calculating as

dataset = setup_contrasts(dataset, contrast_list = list(  c("WT","KO")  ) )

And its output looks like

enter image description here

When this graph title says "vs" in what context its been used? When we say A vs B; generally, we assume A ÷ B

Here in this volcano plot contrast: WT vs KO, do you mean to say your reference is KO or vice versa (i.e WT)? Are these red-color triangles (proteins) more abundant in WT or KO?

Can you help me to understand how this calculation function works please.

limma • 744 views

ADD COMMENT • link updated 14 months ago by Gordon Smyth 50k • written 14 months ago by Wuschel ▴ 10

score 0 · Answer 1 · 2023-02-22

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Gordon Smyth 50k

@gordon-smyth

Last seen 1 hour ago

WEHI, Melbourne, Australia

You will need to ask the msdap people using their github issues page. If you were using limma functions directly, then we could answer your questions, but you are actually using msdap wrapper functions. The limma functions have an unambiguous syntax from which the answer to your question would be obvious, but the msdap package has wrapped them in its own function setup_contrasts with syntax that is not self-explanatory.

ADD COMMENT • link 14 months ago Gordon Smyth 50k

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Thanks Prof. I asked, but no reply yet. If this is Limma, what would be the answer when we say WT vs KO; is that WT ÷ KO or vice versa?

I see "vs" is been used interchangeably in figure legends and if there are no specific labels on the figure, it's hard to understand.

e.g. https://www.nature.com/articles/s41598-021-82533-5 https://journals.plos.org/plosone/article/figure?id=10.1371/journal.pone.0063825.g003 https://www.sciencedirect.com/science/article/pii/S2352340922003092#! https://www.pnas.org/doi/10.1073/pnas.1720447115 https://www.htgmolecular.com/blog/2022-08-25/understanding-volcano-plots

ADD REPLY • link 14 months ago Wuschel ▴ 10

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In the limma documentation, and in my published papers, WT vs KO always means WT - KO where WT and KO represent mean values on the log-scale. A protein with a positive logFC for WT vs KO is higher in WT.

ADD REPLY • link 14 months ago Gordon Smyth 50k