[BioC] Statistics for Diagnostic Microarrays

A.J. Rossini rossini at blindglobe.net
Thu Jul 8 14:49:16 CEST 2004

Sure, but then you've got a high-dimensional "diagnostic statistics"
problem; these are still not fully worked out, though see Margaret
Pepe's recent book on the topic for a start.


"michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk> writes:

> Actually, a lot of the work for pattern recognition is already there -
> from classical statistics and from use with proteomics data:
> -----Original Message-----
> From: Adaikalavan Ramasamy [mailto:ramasamy at cancer.org.uk] 
> Sent: 08 July 2004 13:37
> To: michael watson (IAH-C)
> Cc: BioConductor mailing list
> Subject: Re: [BioC] Statistics for Diagnostic Microarrays
> Dear Mick,
> I think there is a gold field of opportunities for statistics in this
> field. With more and more companies advertising disease-specific chips,
> there are still questions to be answers, namely :
> a) gene selection : Only several hundreds or thousands of genes are
> going to be selected for their discriminating ability.
> b) normalisation  : The assumption that majority (90-95%) of the genes
> unchanged will not hold here. If you are going to use "housekeeping"
> genes, which ones to use and how to use them. So far, the main
> normalisation methods (justifiably) ignore housekeeping genes as they
> vary from sample to sample.
> c) multiple spots : If you are going to spot, say 2000 genes, then you
> can spot 10 of each at random positions on the chip. This not only
> affects the normalisation (highly correlated spots) but also the
> analysis aspect (is there a better approach than averaging?).
> d) classification : How does one assign the probability that a patient
> has a disease given the expression profile of thousands of genes. I
> think we may require pattern recognition techniques or machine learning
> approaches and a large enough learning set.
> e) better classification : Is the diagnostic chip better than existing
> tests (if any) and is it cost efficient.
> Sorry for pointing out more questions than answers but I feel that more
> people should be be asking these before buying/designing a designer
> boutique arrays.
> I think what people are currently doing is using microarrays as
> filtering tool along with other knowledge to obtain a marker
> gene/protien that they can easily test for. The relevant key word is
> metabolonomics.
> HTH, Adai.
> On Thu, 2004-07-08 at 09:12, michael watson (IAH-C) wrote:
>> Hi
>> Obviously the greatest use for Microarrays is for gene expression 
>> studies, but increasingly scientists wish to use Microarrays for a 
>> variety of diagnostic studies, which centre more around "Is it there 
>> or not?" type questions rather than "How much of it is there?".  Does 
>> anyone know of any statistical tools or software that can be used 
>> specifically for diagnostic microarrays?
>> Thanks
>> Mick
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Anthony Rossini			    Research Associate Professor
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
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