This is something I've been thinking about on and off since the first time I ran through a full microarray differential expression workflow in R a few months ago.
I noticed that applying lmFit and eBayes resulted in a number of p-values that are 0. While I acknowledge that there are very many different ways of calculating p-values and that 0 is potentially valid, I have not seen instances in the literature of p-values of 0. It seems more like an artifact from rounding, or something other setting somewhere that I'm missing. I haven't set the number of display significant digits, and everything else is default environment-wise. I see the same values when I write out the results using write.fit.
Please let me know if I'm crazy or just missing something. It's a little awkward doing p-value histograms and such on this data, and then trying to figure out how so many values could be exactly 0 in order to explain the results to others.
Thank you
