SAGE significance

Tim Ritty Tritty at cellbio.wustl.edu
Wed Jun 18 11:25:26 EST 1997


rork at umich.edu (Rork D. Kuick) wrote:

>In "Gene expression profiles in Normal and Cancer Cells" (Science, 23 may 97,
>1268-1272) Zhang, Zhou, Velculescu, Kern, Hruban, Hamilton, Vogelstein,
>and Kinzler, sample a great many transcripts using SAGE from different
>sources and then compare the frequency of transcripts.
> I cannot understand their statistical comparison - their note #8 was
>difficult.  I'd like to think that it not just my problem - I perform
>Monte-carlos to compute ssignificances as well from time to time.
>Does "differences in expression" mean "in the sampled SAGE
>transcripts" or "in mRNA molecules from which we are sampling"?  

	As I read the article, "differences in expression" MUST mean: among
the sampled SAGE transcripts.  This is because they are comparing the
data they found for two (or more) groups of cells.  They would not
know 289 transcripts were expressed at higher levels in one group
versus another if they did not have information that they could
compare - therefore it cannot be "in (total) mRNA molecules from which
we are sampling."

Tim




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