[BioC] Does hist (affy) function work on probe-pair values or probe-set values?

James W. MacDonald jmacdon at med.umich.edu
Tue Oct 13 16:07:29 CEST 2009

Hi Javier,

Javier Pérez Florido wrote:
> Dear list,
> I've tried to use hist (affy package) to check the quality of two 
> different sets of CEL files from the same experiment:
>     * The original set of CEL files.
>     * The permuted set of CEL files (raw signal intensities for each
>       probe pairs were randomly permuted for each array to create
>       uninformative CEL files)
> When hist function is called using the raw original data and the raw 
> permuted data separately, the histograms of both set of CEL files are 
> the same, even if the probe-pair values are randomly changed in the 
> second set. This fact suggests that the density graph is built using the 
> probe-pair values instead of probe-set values.
> But, after a preprocessing method is used on both sets (for example, 
> VSN), the results are quite different: the histograms are not the same 
> and the permutation can be observed easier in the second set. So, this 
> suggests that:
>     * The hist function builds the density graph using the probe pair
>       values when an Affybatch object is used (that is, raw data).
>     * The hist function builds the density graph using the probe set
>       values when an expression set object is used (that is, after
>       preprocessing).
> Is that correct?

Of course! The AffyBatch object contains only raw data and the 
ExpressionSet contains only processed data, so what else could be used 
in either case?



> Thanks in advance,
> Javier
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618

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