Hi Ingrid,
>
> - When annotating my data should I use the lumi annotation packaged
or is can
> I use the other Illumina annotation packages?
Yes, you can directly use other annotation packages if you did not
transfer
the Target ID as nuID.
> - I use the lumi package with bead summary data. How can the VST
take
> advantage of the number of replicates on an Illumina array when it
is used on
> bead summary data (as you say in the user guide)?
The vst using the mean and variance of the beads for variance
stabilization.
The basic idea is the same as vsn (see vsn package), but we take
advantage
of the multiple beads (usually about 30) of the same probe within each
microarray. A manuscript is still under review. Hopefully, it can get
published soon.
> - How do you produce the plot in figure 9 in the user guide?
>
I am not sure what you mean because the user guide already provides
the code
of producing the picture.
Pan
