Hi,
  This may be a generic question, not necessarily related to the usage of R and bioconductor. The question is: for microarray experiment, suppose I have 50 normal and 50 cancer samples. I want to find some sample outliers which may come from different resources due to:
1. Mislabelling, i.e, mislabel cancer into normal or normal into cancer
2. Misbehavior, i.e, some normal samples are actually sick or have heart attack, although they don't have cancer. 

Should I do gene selection or not before doing outlier removal? Sometimes I find some samples are identified as outliers using 200 genes, other samples will be identified as outliers if I use 50 or 20 genes. Normally in microarray experiment, what is the percentage of genes affected by treatment or unnormal conditions? 

  Thanks,
  James


 		
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