[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
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
> 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,
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James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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