



Thanks, Naomi,

I am asking 2 things:

First, how to compare the cross-correlations among genes in
two gene sets of the same size. This includes both senarios you pointed out,
both the all-higher-than-all one and not so well-defined one. I want some
statistical test that gives a summary p value on the comparison.

Second, how significantly correlated the genes in one
particular set are relative to all genes. This is a problem related to the
first one, in that we can always randomly pick up control sets of the same size
up from the whole gene list.

Thanks a lot!

Heyi



--- On Thu, 2/26/09, Naomi Altman <naomi@stat.psu.edu> wrote:
From: Naomi Altman <naomi@stat.psu.edu>
Subject: Re: [BioC] Test on correlations among a group of genes
To: xiaoheyiyh@yahoo.com
Cc: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch>
Date: Thursday, February 26, 2009, 11:38 PM

Although I think the concept is clear in some special cases, such as 
all the cross-correlations among genes in 1 set being
higher than all the cross-correlations in another, I am not sure you 
are asking a well defined question.

e.g.  Set 1:      1  .6  .6             Set 
2:    1.  .7  .5
                       .6  1  .6                          .5   1   .7
                       .6 .6   1                          .7  .5   1

Which set is more highly correlated?

--Naomi



At 05:58 PM 2/26/2009, you wrote:




>Dear list,
>
>I have an expression microarray dataset. I would like to compute
>whether the correlations among a group of genes are significantly higher
>compared to all genes. What is the proper statistical test to use? 
>Note that the
>correlation coefficients (a matrix) for the target gene group or the 
>background
>whole set are not all independent, which makes the test a little 
>trickier. I would
>appreciate any thoughts/suggestions.
>
>
>
>Heyi
>
>
>
>
>
>
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111




      
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