Hi

Thank you for your quick answer.

Unfortunately I am still a bit confused regarding the VST. I understood the part regarding the vst using the mean and variance of the beads for variance stabilization, but then you say: “we take advantage of the multiple beads (usually about 30) of the same probe within each microarray.” Do you mean that through the mean and variance you take advantage of the around 30 beads. If not how do you get the information about the 30 beads when using the bead summary data?

Regards,
Ingrid




 
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





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