[BioC] Test on correlations among a group of genes

[Naomi Altman]

I do not know how to do the test, but I have reservations about using KS.
The correlations are correlated.  The test statistic for the KS test seems
likely to be sensitive to this.

--Naomi

At 10:19 AM 2/27/2009, Robert Castelo wrote:
>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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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