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?

Thanks in advance,
Javier


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