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. When should I apply a detection filter, relative to the other steps in the process?
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 for the timing of applying a detection filter?