[BioC] combineAffyBatch for HG-U133A and HG-U133Av2 GeneChips

[David Lee Duewer]

>> I would like to remove unwanted probeset from the resulting $dat
>> object prior to applying rma or any other expression summary method.
>
>I think it should not make much of a difference whether you remove these 
>probesets before or after RMA, since the R in RMA stands for "Robust".

Umm, no matter how nominally "robust" a method, you are always better off explicitly getting rid of KNOWN unwanted-signal (ie, noise) rather than relying on the methodology ignoring it.  Even medians can be badly perturbed by the inclusion of relatively small proportions (10-15%) of asymmetric (all high or all low) "non-informative signal".

D

David Lee Duewer
Research Chemometrician
National Institute of Standards and Technology
100 Bureau Drive Stop 8390
Gaithersburg, MD  20899-8390
USA


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