[BioC] Loess Normalization of Spotted Chip

[Wolfgang Huber]

Hi Tzulip,

you can try the function vsn in the package of the same name. If y is a 
matrix of size (no.probes) x (no.chips), and pins is an integer vector 
of length (no.probes) with values 1, 2, .... that code for the print-tip 
ID, then

ny1 <- vsn(y, strata=pins)

should do the job. You can compare this to

ny2 <- vsn(y)

for a single-channel normalization "without" print-tips. For details, 
please see the vignette. I'd be interested in your experience with this.

library(vsn)
openVignette("vsn")

Best wishes
   Wolfgang


Tzulip Phang wrote:
> We are very interested in eliminating the print-tip effects for our 
> single channel data.  Do you know if any group have tried to accomplish 
> that on the single -channel oligo chips data?
> 
> Thank you
> 
> Tzu
> 
> Gordon K Smyth wrote:
> 

-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/abt0840/whuber