[BioC] Affymetrix preprocessing, MAS5 vs. RMA

[Dozmorov, Mikhail G. (HSC)]

Hello,

I'm learning basics of importing Affy's .cel files to R, and do it with affy library:
	R> Data <- ReadAffy()
When I do preprocessing
	R> eset <- rma(Data) OR eset <- mas5(Data)
I'm getting very different expression values.
	From MAS5:
ID	21.CEL	33.CEL	36.CEL
1415670_at	2494.54	2576.29	2240.92
1415671_at	6292.17	5013.13	3075.89
1415672_at	6727.66	5858.31	5690.70
1415673_at	567.38	718.02	875.25
	From RMA, Antilogged from Log2
ID	21.CEL	33.CEL	36.CEL
1415670_at	74.16	69.30	59.08
1415671_at	191.52	171.38	94.30
1415672_at	194.18	199.57	175.13
1415673_at	14.93	13.16	21.50

Can't find any explanation why it could happen. And what to use? Please, advice! Thank you. Mikhail.