Interesting problem (at least to me).  I am working with circadian rhythm data of activity levels -- activity measurement is made every 15 seconds over many days by an accelerometer attached to the subjects wrist (called an actigraph).  Not genetic data but conceptually similar.
   
  I have been using functional data analysis to turn the activity values into smoothed functions and then analyzing the functions.  Take a look at http://ego.psych.mcgill.ca/misc/fda/
   
  If you have gene exprssion at enough time points you might be able to model a single genes expression profile as a function and then look for variation among genes over time.
   
  Let me know if you want to discuss further.
   
  Bill Shannon, PhD
  Associate Professor of Biostatistics in Medicine
Washington University School of Medicine
http://ilya.wustl.edu/~shannon

  
BioRankings, LLC
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Lewin Eisele <lewin.eisele@uni-due.de> wrote:
  Dear list,

I would like to analyse circadian rhythms in gene expression. I found some
references regarding a methodology called "single cosinor method" with which
such an analysis should be possible.

Does anyone have experience with this kind of analysis, especially with the
cosinor method? Can anyone point me to references? Is there a R or
Bioconductor package to help in this kind of analysis?

I hope, this is not too much off topic,

Thanks
Lewin



Dr. med. L. Eisele
Klinik für Hämatologie
Universitätsklinik Essen
Hufelandstr. 55
45122 Essen

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