From d0911a04958a04042da02a334ccc528dae79cc17 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 27 Mar 2015 20:28:51 +0000
Subject: Removed everything from 'web' directory except genofiles and renamed
the directory to 'genotype_files'
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PowerPoint Presentation - Complex trait analysis, develop-ment, and
genomics
lThe App transcript neighborhood
Question: How many transcripts have correlations >0.7? What does this imply.
The answer is a strong
Yes. A very large number of transcripts have correlations above 0.7 (absolute
value) with App mRNA. The precise number today is 208. But this will change
as we add more strains and arrays. In any case, this is a fairly large number
and all of these correlations are significant at alpha .05 even when
correcting for the enormous numbersof tests (12422 tests).
What does this imply?
That there can be
massive codependence of expression variance among transcripts. App is NOT an
isolated instance. This is improtant biologically and statistically. From a
statistical perspective, we would like to know how many ÒindependentÓ test we
effectively are performing when we use array data in this way. Are we testing
12000 independent transcripts or just 1200 transcriptional ÒmodulesÓ each
with blurred boarders but each with about 10 effective members. There is no
answer yet, but we probaby have a large enough data set to begin to answer
this question.
