[BioC] Large # of significant genes with SAM

[Vincent Detours]

Dear all,

Your expert opinion are most welcome on the following.

I am finding using siggenes' SAM @ q<0.05 (26 samples on cDNA chips)
that 37% of all genes are regulated with respect to patient-matched
"normal" tissues in somme tumors not particularly known for huge
aneuploidy. Looking at another data set from the same cancer but
collected by another group on indepentent samples on Affy, I got 34%.
The number seems to hold.

How to interpret this? Are really 30% of the genes disturbed, even to
a small extent, in these tumors? Could SAM do something wrong? If yes,
how to verify it?

Any advise, shared experience, references, etc. are welcome

Cheers

Vincent


------------------------------------------
Vincent Detours, Ph.D.
IRIBHM
Bldg C, room C.4.116
ULB, Campus Erasme, CP602
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B-1070 Brussels
Belgium

Phone: +32-2-555 4220
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E-mail: vdetours at ulb.ac.be

URL: http://homepages.ulb.ac.be/~vdetours/