At which step should I apply a detection filter when preprocessing microarray data? (Before/After normalization, batch effects removal)

Question

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?

virtualxtc · Answer

My comment above still stands; provided your detection filter doesn't rely on your data being normalized, your detection filter can exist anywhere.

However, since it seems you know that you want to run a PCA, and know all the normalization's you'd like to try already, it is simplest to run all of your normalization first, that her than having to filter out high scoring vectors that appear to be caused by inter-sample variation.

At which step should I apply a detection filter when preprocessing microarray data? (Before/After normalization, batch effects removal)

One Answer

Add your own answers!

Ask a Question