[BioC] Test on correlations among a group of genes

[Robert Castelo]

hi Heyi,

i'd try to look at the empirical cumulative distribution functions of
the absolute values of the correlations and test if the difference
between the two enclosed areas by these functions are significanly
different. i'm not completely sure about what test should you use (maybe
somebody else in the list has a clear hint!) but i think the ks.test
would do.

cheers,
robert.



On Fri, 2009-02-27 at 07:29 -0800, heyi xiao wrote:
> 
> 
> 
> 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 at stat.psu.edu> wrote:
> From: Naomi Altman <naomi at stat.psu.edu>
> Subject: Re: [BioC] Test on correlations among a group of genes
> To: xiaoheyiyh at yahoo.com
> Cc: "bioconductor at stat.math.ethz.ch" <bioconductor at 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
> >
> >
> >
> >
> >
> >
> >
> >         [[alternative HTML version deleted]]
> >
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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
> 
> 
> 
> 
>       
> 	[[alternative HTML version deleted]]
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