[BioC] Filtering before differential expression analysis of microarrays - New paper out
Steve Lianoglou
mailinglist.honeypot at gmail.com
Wed Jan 14 17:10:38 CET 2009
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
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