[BioC] Affymetrix preprocessing, MAS5 vs. RMA

[Daniel Brewer]

I believe that RMA produces expression levels that have been log2'ed
whilst MAS5 does not.  Even so you still can't compare the values
directly.  It is generally thought that MAS5 should be avoided, even
Affymetrix recommend PLIER (another algorithm produced by Affy) over MAS5.

Dan

Dozmorov, Mikhail G. (HSC) wrote:
> 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.
> 
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-- 
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Daniel Brewer, Ph.D.

Institute of Cancer Research
Molecular Carcinogenesis
MUCRC
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Tel: +44 (0) 20 8722 4109

Email: daniel.brewer at icr.ac.uk

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