12.0 years ago by
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
> Cy5 in upper left corner). I have applied loess normalization, but
> correct this 'bias". I can't really apply printtiploess. Could VSN
> quantile normaliztion be applied here or could suggest a method to
> this data?
A couple of questions, first. What is on the array (what design)?
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
from neighboring probes, so assuming the probes are randomly
the slide relative to genomic position, there shouldn't be a big
a percentage of the slide is missing/bad.
Finally, if you think of these spots as "bad", you can set the weights
those specific probes to zero and use limma to do the normalization,
actual normalization you want to do is going to depend on the