Hi,
On May 7, 2009, at 10:53 AM, Steve Goldstein wrote:
A simple permutation test could be done by selecting random sets of
intervals "matching" the query intervals and counting the number of
overlaps with the reference intervals. Each random set of intervals
could be picked so that the number and size of the intervals was the
same as the query. A general implementation of the method would
need to know the length of each chromosome.
I was just about to suggest something similar, though I didn't think
to consider chromosome length ... can you give some intuition as to
why that's important for this question?
I guess you'd expect more "collisions" to happen at random on a
chromosome if it's longer, but I think in general one wouldn't be
interested in finding the number of reads that "collide" between two
experiments for a particular chromosome as you might be interested in
just seeing how many collisions happen over the entire extent of the
genome ... so is it helpful to think of the genome as broken up into
chromosome-pieces, or would it suffice to simply think of it as being
one contiguous length of sequence for this purpose?
Of course, if the null hypothesis for this permutation test (the
sets intervals are not related) is rejected, then you have to think
about the next questions: To what degree are the set related?
I'm picturing the aligned reads as painting small lines on a large
canvas (the entire canvas is the genome in this analogy).
If your first expt is painting red lines.
Your second expt is painting in blue lines.
The question is how much of the canvas is purple.
So it "feels" like some sort of an enrichment test to me, could you
try to answer this question in a similar fashion to GO enrichment, via
some sort of hypergeometric test? That's not exactly correct ... just
brainstorming is all.
Where do they differ and where are they the same?
I'll stop with my speculation here ... :-)
-steve
--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Medical College of Cornell University
http://cbio.mskcc.org/~lianos
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