[BioC] checking multi-modalities in histograms
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
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
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,
> [[alternative HTML version deleted]]
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
More information about the Bioconductor