Biology Stack Exchange is a question and answer site for biology researchers, academics, and students. Join them; it only takes a minute:

Sign up
Here's how it works:
  1. Anybody can ask a question
  2. Anybody can answer
  3. The best answers are voted up and rise to the top

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


  • Loess normalization between samples
  • ComBat

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

share|improve this question

Your Answer


By posting your answer, you agree to the privacy policy and terms of service.

Browse other questions tagged or ask your own question.