About question 4

[Selen Uguroglu]

Hi all,

As a response to Jose's question below, in problem 4, you are only required to report p values to compare subgraphs.

Cheers,
-Selen

---------------------------- Original Message ----------------------------
Subject: Q4.e
From:    "Jose Juan Tapia" <jjt...@pitt.edu>
Date:    Sun, April 10, 2011 3:05 pm
To:      computational-ge...@googlegroups.com
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In question Q4.e they ask us to calculate a way to score different subgraphs
using a binomial distribution. While the pvalue that we would obtain from
such evaluation can be used for comparing between subgraphs as indicated in
the homework, it'd also be natural to use it
as a test of significance for the different timepoints in a cluster (e.g.
when we calculate individual pvalues for each time point in a cluster,
should a pvalue be small enough it means it's not signiciant; for example it
could mean that at that particular timepoint it just happened that a lot of
genes were being activated, and as such those edges aren't really a good
indicator for correlation), so we're not sure if this is also expected from
our implementation.

Should we take this into account for our programs? In such case, what would
be the required significance cutoff point.

Yours,