[BioC] checking multi-modalities in histograms

[Javier Pérez Florido]

Dear Wolfgang,
Thanks for your reply.
The data I am going to test for bi-modalities are raw data, without 
preprocessing. For this purpose I think it is ideal to use bimodalIndex 
function from ClassDiscovery package. It tests for bimodalities using 
the information-based BIC criterion.
I know that there are more quality metrics such as boxplots, MA plots, 
NUSE, etc...The use of histograms is complementary to all of them and 
all I need is something that says that, maybe, a CEL file isn't good due 
to such bi-modalities, taking into account the rest of quality metrics.

Thanks again,
Javier



On 30/03/2010 14:54, Wolfgang Huber wrote:
> Dear Javier
>
> note that the number of modes of a distribution
> - can depend on the normalisation (before or after log-transformation; or whether background correction was done and how)
> - is impossible to determine from a finite sample without further assumptions (essentially a smoothing bandwidth)
>
> Besides these (significant) practical difficulties, I am also doubtfulof the usefulness, in terms of sensitivity and specificity, of this criterion for array quality diagnostics. If you see two modes, they would most likely be associated with a covariate, such as row,  column, spatial position on the array. Then, if you find that this co-variate is quality-relevant, then I would advise checking for significant effects of that covariate even on arrays where the distribution looks uni-modal.
>
>         Best wishes
>             Wolfgang
>
> Mar 29, 2010, alle ore 6:14 PM, Javier Pérez Florido
>
>    
>> 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
>>
>>
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>>
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