Gene filtering in microarray data normalized with the SCAN method

Question

[Ld_60]

Hi everyone,

I am working with affymetrix microarray data, and I am willing to apply the SCAN (Single-Channel Array Normalization) method to normalize the data, as I want the normalization to be applied to individual samples instead of a batch of arrays.

I am wondering which type of gene filtering method (variance, average signal,... etc) can be used in this case, what filtering rules (threshold values corresponding to each filtering method), and when to apply the filtering step (i.e. before or after normalization) ?

Thank you very much for your help.