Normalizing with RMA and filtering with mas5calls (affymetrix arrays)

Question

[aguasalina]

Hi all,

I'm working with affymetrix arrays and I'm wondering if normalizing data with RMA and then filtering expression data with mas5calls (Presence/Absence calls) is a correct methodology. Somebody knows anything about it?

Thank you in advance!

Answer 1

[poisonAlien]

Hi,

Yes its perfectly valid method to do so. It helps to remove those 'noisy' probes with low detection level. I have seen people removing probesets showing Absence in at-least 50% of the samples.