Hi, I am trying to use the Dilution data for some alternative plotting. I discovered that the Dilution data is much different from what is documented in affy.pdf (the vignette). So now mva.pairs(Dilution[,1:3]) no longer works. Is this because the structure is changing toward affy2, and the plob data structure is not going to be supported? I want to reproduce the points in the mva.pairs plot with hexagon bins to see if the structure is clearer. How do i get the same quantities as in the vignette? Do I have to go back to affy_1.0 ? Nicholas

On Wed, Nov 06, 2002 at 02:15:31PM +0800, Nicholas Lewin-Koh wrote: > Hi, > I am trying to use the Dilution data for some alternative plotting. I > discovered that the Dilution data is much different from what is > documented in affy.pdf (the vignette). So now mva.pairs(Dilution[,1:3]) > no longer works. Is this because the structure is changing toward affy2, > and the plob data structure is not going to be supported? I want to > reproduce the points in the mva.pairs plot with hexagon bins to see if > the structure is clearer. How do i get the same quantities as in the > vignette? Do I have to go back to affy_1.0 ? > > Nicholas > The classes Plob and Cel.container are no longer part of the package. We believe that the new class AffyBatch, which replaces both of them, will benefit all (despite the adaptation time for people used to the old classes). The current (rough) vignette for the new package is called affy2.pdf. It should move to affy.pdf very soon. The example you mention write now: mva.pairs(intensity(Dilution)[, 1:3]) L.