Hi Steve,
  Thank you very much for your help. Know it is clear for me. I can do the
array normalization (like rma) on the whole data set. Then I have to split
the dataset and I can do things like filtering of genes or gene
standardization only on a training set.
  I was confused after reading a book "Bioconductor Case Studies". In the
chapter about supervised machine learning they performed non-specific gene
filtering and gene standardization on the whole dataset. But I would rather
trust that you are right.

Theresa Brandt

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