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I recently read a paper describe their result with MA-contour plots, I did some searches, but most of the information I could get was about the results of contour plots, which seemed to be different from the data in the article. Is this a variant of MA-plot?

See Figure 2g of https://doi.org/10.1101/2023.08.21.554109

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$M$ and $A$ are two expressions for microarray fluorescence readouts, specifically the ratio of intensity between two colour channels and the average of both intensities - usually in the log scale. Wikipedia has a lot of details.

To answer the specific question on the contour, yes, they likely converted a scatter plot into a density. You can see they did the same with more axis annotations in figure 2d, and in both cases the intensity scatter plot (in original scale) is right above the MA contour.

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  • $\begingroup$ I have a bit confusing about the contour, I understand that a contour need three axis (X, Y, Z) and convert it to 2D plot, however as a MA plot, its seem that we only have two axis? $\endgroup$
    – zhang
    Commented Nov 2, 2023 at 11:48
  • $\begingroup$ The Z is the density at that point, you can calculate it as the number of observations that lie within each cell of an X-Y grid. I'm not sure if there's an R function to do it for you but there's bound to be some package out there. $\endgroup$
    – PBulls
    Commented Nov 2, 2023 at 12:07

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