What is the correct order of flooring-normalization-batch correction for microarrays ?

Question

[Aspire]

I am trying to learn and understand the correct order of data processing steps for microarrays.

• In what order should one apply flooring (setting all values below a threshold to that threshold's value), normalization, and batch correction?

Answer 1

[Mohammad Rezaei]

As far as I know, setting the threshold value is the first step for microarray data analysis. This step deletes the non-expressed genes (noises in the raw data). If you don't delete these genes at the first step, their expression values affect the result of normalization and DEG analysis. But about the batch correction, the batch effect removal methods (e.g. sva) are kinds of normalization. If your data has batch effects and you remove them, you performed a normalization on the raw data, and you should not perform another normalization on the normalized data (e.g. quantile normalization).