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ByrumLab / proteoDA

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Tim vignette edits #215

Closed tjthurman closed 1 year ago

tjthurman commented 1 year ago

This PR contains pretty extensive edits to the vignette to flesh it out into a detailed tutorial. It moves some files around to get things right with R CMD check and make sure users can use the example data files we provide, and it adds in the images to fix #200 .

tjthurman commented 1 year ago

OK, made edits in response to these comments. I cleaned up lines 112 and 137. I tried to clarify line 135 more: from the point of view of the limma models, a 0 is saying that we know the protein is not present (it is including 0 in the logFC calculations). So I tried to re-write it to make it clearer: in the "model world" a 0 is treated as if we know the protein is not present, but in the "real world" this is rarely the case, so we shouldn't use 0s unless we're sure.

ByrumLab commented 1 year ago

Use an example of a Knockout experiment for the zero when you have evidence that this protein has been removed. Otherwise it is still not clear.

tjthurman commented 1 year ago

OK, a little more clarification that is hopefully correct!