On Thu, Jan 22, 2009 at 3:47 PM, Dozmorov, Mikhail G. (HSC) <
Mikhail-Dozmorov@ouhsc.edu> 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.
>

Each normalization method is indeed different.  They should and will produce
different results.  There is an extensive literature on different methods of
normalization and preprocessing for Affy that you can read to get the
details.

I would say that most people would not use MAS5 anymore.  RMA is a good
alternative.

Sean

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