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I am trying to understand what is the best practice when preprocessing microarray data using a detection filter (on scanner p-value). Suppose I have a microarray dataset that I have to normalize with Loess and correct with ComBat. In which order have I to apply detection filter with regards to the other operations?

In my experimental design, I have two pipelines to test:

  • Normalize per sample between 0 - 1
  • ComBat
  • Loess normalization between samples

and

  • Loess normalization between samples
  • ComBat

Is there any best practice to apply when dealing with detection filter? Where have I to apply detection filtering?

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