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Perhaps you could clarify. Is this an MAplot() command called on an AffyBatch, exprSet, PLMset? Generally speaking these should all be on log2 scale, but looking at your numbers suggests closer to something that has been double logged. Ben On Mon, 2005-11-14 at 13:45 -0600, Simon Lin wrote: > When doing the MAplot in the affyPLM package, what exactly is the unit > of the X-axis? It ranges from 2.5 to 4. Seems an average of the log10 > intensity? But it is too low. > > A suggestion: the plot is generated way too slow for U133plus2 files. > Maybe a random sampling of 1000 points is sufficient for QA purpose. > > Simon > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor