[BioC] checking multi-modalities in histograms

Kevin Coombes kevin.r.coombes at gmail.com
Mon Mar 29 19:41:49 CEST 2010

The Mclust R package has one set of tools to do this.

I would also advise you to take a look at the bimodality index that we 
defined in
  Wang J, Wen S, Symmans WF, Pusztai L, Coombes KR.
   The bimodality index: a criterion for discovering and ranking bimodal 
signatures from cancer gene expression profiling data.
  Cancer Inform. 2009 Aug 5;7:199-216.  PMID: 19718451
along with the editorial
  Ertel A.
  Bimodal gene expression and biomarker discovery.
  Cancer Inform. 2010 Feb 4;9:11-4.  PMID: 20234772

An R package (ClassDiscovery) that includes a function to compute the 
bimodality index can be obtained from


Javier Pérez Florido wrote:
> Dear list,
> Histograms are usually used to check the quality of microarray 
> experiments. If there are bi-modalities in a particular array, it is a 
> candidate to exclude it from the experiment. It is easy to check 
> bi-modalities or multi-modalities visually, but I would like to know if 
> there is a way (using a statistical test or something) to check 
> multi-modalities using the data returned by the hist function.
> For an Affybatch object, hist function returns the X and Y values, but 
> that's all, it doesn't return the variables breaks, counts, etc as it is 
> said in the help manual for hist. So, I have two questions:
>     * Is there a test to check for multi-modalities in histograms?
>     * Is there a way to know the cells and the number of values per cell
>       used by hist to check for multi-modalities in a rudimentary way?
> Thanks again,
> Javier
> 	[[alternative HTML version deleted]]
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