[BioC] checking multi-modalities in histograms

Javier Pérez Florido jpflorido at gmail.com
Tue Mar 30 09:44:51 CEST 2010

Thanks Kevin,
I had a look at the Mclust package and I don't see any function that 
could help me on this, could you please be more precise?

On the other hand, I also had a look at the bimodalIndex function in 
ClassDiscovery package and I don't know which parameter of the BI 
variable is interesting for me. Moreover, I would like to check for 
bi-modalities or multi-bimodalities on affybatch objects (the hist 
function uses affybatch objects), which, as far as I know,  cannnot be 
handled by the bimodalIndex function.

Any suggestions?

On 29/03/2010 19:41, Kevin Coombes wrote:
> 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
>    http://bioinformatics.mdanderson.org/Software/OOMPA/
> Best,
>    Kevin
> 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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