Hi all, 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?