[BioC] Normalization of 2 color Nimblegen array

[Sean Davis]

On 3/16/06 7:53 AM, "Khan, Sohail" <khan at cshl.edu> wrote:

> Dear list,
> 
> I have a two color Niblegen array which has a slight spatial effect (higher
> Cy5 in upper left corner).  I have applied loess normalization, but it doesn't
> correct this 'bias".  I can't really apply printtiploess.  Could VSN or
> quantile normaliztion be applied here or could suggest a method to normalize
> this data?

Sohail,

A couple of questions, first.  What is on the array (what design)?  Second,
what kind of experiment (chIP/chip, CGH, expression)?

In general, we have found nimblegen arrays to be pretty robust against
spatial artifacts, simply because one is so often able to use information
from neighboring probes, so assuming the probes are randomly distributed on
the slide relative to genomic position, there shouldn't be a big problem in
a percentage of the slide is missing/bad.

Finally, if you think of these spots as "bad", you can set the weights for
those specific probes to zero and use limma to do the normalization, but the
actual normalization you want to do is going to depend on the questions
above.

Sean