Dear list,
I have few questions about lumi package:

  * How can the control plots be interpreted? For example:
    plotControlData, plotHousekeepingGene and plotStringencyGene. I
    don't know what the scenario to detect bad samples should be when
    using these plots.
  * What is the meaning of the density plot of coefficient of variance?
    How can bad arrays be detected? Similar to traditional density plots
    (that is, different distributions)?
  * In lumi vignette, as well as in other packages, it is recommended to
    work with probe information instead of gene information. For
    example, when the sample probe profile file is opened, there might
    be several probes that target the same gene. If working with such
    sample probe profile file and after variance stabilizing transform
    and normalization are made, the expression set generated can be used
    as the input of limma. My question is: does limma detect
    differentially expressed probes or differentially expressed genes?
     From a practical point of view, is it the same?


Thanks,
Javier


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