[BioC] Filtering before differential expression analysis of microarrays - New paper out

[Steve Lianoglou]

Hi Gordon,

As someone who has been dealing more and more with raw data, I always  
appreciate detailed answers from the masters, such as the one you just  
wrote. Even after reading several of the published articles regarding  
these normalization practices, I always find these less formal emails  
quite helpful.

That said, one point you mention isn't exactly clear to me, and I'm  
wondering if you could elaborate just a bit here:

> Filtering non-expressed probes tends not be emphasised on this list  
> because users of this list are often sophisticated enough to use  
> variance stabilizing normalization methods such as rma, vsn, normexp  
> or vst.  This means that low-expression filtering is done more for  
> multiplicity issues than for variance stabilization, and therefore  
> often doesn't make a huge difference.  When using earlier  
> normalization methods such as MAS for Affy or local background  
> correction for two-color arrays, expression-filtering is absolutely  
> essential, because the normalized expression values are so unstable  
> at low intensity levels.


When you say "... low-expression filtering is done more for  
multiplicity issues than for variance stabilization", what exactly do  
you mean by "multiplicity issues"?

Thanks,
-steve

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University

http://cbio.mskcc.org/~lianos