[BioC] checking multi-modalities in histograms

Wolfgang Huber whuber at embl.de
Tue Mar 30 14:54:34 CEST 2010

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

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
> 	[[alternative HTML version deleted]]
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