[BioC] Differential expression

[Richard Friedman]

Dear Makis,

	I think the idea is that the normalization methods must assume
that the expression is basically the same between the types of
cells in order to work. This might not always be in fact the case,
but if it isn't, then the use of methods like quantile normalization
to reduce technical variation leaving only biological
normalization become suspect.

	Anyway, that's my take. I would love to hear from
people more knowledgeable than myself on this issue.

Best wishes,
Rich

On May 26, 2006, at 11:06 AM, E Motakis, Mathematics wrote:

> Dear all,
>
> I am working on two colours microarray experiments and, from a set of 
> 42000
> genes, I would like to identify the differentially expressed ones. I 
> have
> read several articles on this issue and most of them imply that the 
> number
> of differential expressed genes in such experiments should be a small
> number (compared to the whole set).
>
> Could anyone tell me why this is correct? What if I find half of the 
> genes
> to be differentially expressed according to the t-test p-value?
>
> I am not discussing the issue of p-values and q-values yet. I am asking
> only about why most of the papers imply a low number of differentially
> expressed genes.
>
> Thank you,
> Makis
>
>
> ----------------------
> E Motakis, Mathematics
> E.Motakis at bristol.ac.uk
>
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------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist
Herbert Irving Comprehensive Cancer Center
Oncoinformatics Core
Lecturer
Department of Biomedical Informatics
Box 95, Room 130BB or P&S 1-420C
Columbia University Medical Center
630 W. 168th St.
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(212)305-6901 (5-6901) (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/


"Cartesian duelism is when somebody told Decartes that he didn't think
therefore he was, and Descartes challenged him to a duel".
-Isaac Friedman, age 16