At Which Step Apply A Detection Filter When Preprocessing Microarray Data? (Before/After Normalization, Batch Effects Removal)

Question

[fbrundu]

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

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?

Thanks

Answer 1

[Sean Davis]

Consider filtering on per-feature variance rather than detection p-value. I would apply a filter immediately prior to differential expression analysis. That said, I do not know that there is a "best practice" for all datasets and platforms.