[BioC] Large # of significant genes with SAM

[Naomi Altman]

It always pays to look at the actual numbers, and also plot the data.

Perhaps I am unusually careless, but most of the time when I get unexpected 
results, I have made a mistake - e.g. read in the flags instead of the 
expression values, or that type of thing.

--Naomi

At 06:56 AM 5/9/2005, Vincent Detours wrote:
>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
>808 route de Lennik
>B-1070 Brussels
>Belgium
>
>Phone: +32-2-555 4220
>Fax: +32-2-555 4655
>
>E-mail: vdetours at ulb.ac.be
>
>URL: http://homepages.ulb.ac.be/~vdetours/
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://stat.ethz.ch/mailman/listinfo/bioconductor

Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Bioinformatics Consulting Center
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111