Closed tjthurman closed 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.
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.
OK, a little more clarification that is hopefully correct!
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 .