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.

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 [[alternative HTML version deleted]]

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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}