[BioC] Dealing with artifacts on Affy chips.

[Gareth Hughes]

Dear all, 

  Are there any common methods that deal with artifacts that appear on
affymetrix arrays?  Some of our HGU133A arrays have 'comet-like' high intensity
regions.  I've isolated the probes contained within these artifacts and was
wondering if a 'mask file' could be created in R and these chips re-integrated
back into the original dataset?  I'd like to include these chips in functions
such as rma and hclust etc.

Kind regards,

Gareth.


Gareth Hughes
Bioinformaticist
Institute of Medical Genetics, UWCM.

Email : hughesgp at cf.ac.uk
Tel : 029-2074-4837