I have a group of protein expression levels across three different conditions. What I want is to present the expression level of individual proteins across conditions as they are on X, Y and Z axis and construct dot maps and see if I could get anything interesting from this. Anyone have ideas?
You can use Correspondence Analysis for this (there are R packages that do it for you). You'll need a data matrix with your protein expression levels (they have to be positive values), where you have, say, proteins as rows and conditions as columns. The technique finds the optimal projection along two principal axes (2 dimensions are enough for three conditions). The plot contains both conditions and proteins, and you can see associations between them. The first paper that did this for expression data is
http://www.pnas.org/content/98/19/10781.long
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