Hello, I wants to compare expression measures, which was computed with MAS and RMA. But I noticed that the expression-values are very different. e.g.: Expt1_R1.CEL: Gen: 1007_s_at RMA: 8,06941 MAS: 236,16853028 1. How can I interpret this difference? 2. And which mathematical methods for comparison between preprocessing can I use? thanks, Mohammad Esad-Djou Interdisciplinary Centre for Bioinformatics Leipzig, Germany ______________________________________________________________________ ____ Erweitern Sie FreeMail zu einem noch leistungsstarkeren E-Mail- Postfach!

Hi Mohammad, If you look at the description of the functions ?rma and ?mas5 , you'll see that RMA gives you the log2 values, whereas MAS5 leaves the values in the original scale. Use this to convert the MAS5 values into log2 scale (mas5.demo is an eset): exprs(mas5.demo) <- log2(exprs(mas5.demo)) Cheers, Jenny At 01:57 PM 1/4/2006, Mohammad Esad-Djou wrote: >Hello, > >I wants to compare expression measures, which was computed with MAS and RMA. > >But I noticed that the expression-values are very different. > >e.g.: Expt1_R1.CEL: Gen: 1007_s_at > >RMA: 8,06941 > >MAS: 236,16853028 > >1. How can I interpret this difference? >2. And which mathematical methods for comparison between preprocessing can >I use? > >thanks, >Mohammad Esad-Djou > >Interdisciplinary Centre for Bioinformatics >Leipzig, Germany > > >_____________________________________________________________________ _____ >Erweitern Sie FreeMail zu einem noch leistungsstarkeren E-Mail- Postfach! > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu

On 1/4/06 2:57 PM, "Mohammad Esad-Djou" <shahrgol at="" web.de=""> wrote: > > Hello, > > I wants to compare expression measures, which was computed with MAS and RMA. > > But I noticed that the expression-values are very different. > > e.g.: Expt1_R1.CEL: Gen: 1007_s_at > > RMA: 8,06941 > > MAS: 236,16853028 > > 1. How can I interpret this difference? MAS is not in log2 units. RMA is in log2 units. > 2. And which mathematical methods for comparison between preprocessing can I > use? One place to look would be the affycomp package. However, you might want to look at the literature a bit before going too far; some of these comparisons have been done already with tightly controlled experiments. Hope that was what you were asking.... Sean

Mohammad Esad-Djou wrote: > Hello, > > I wants to compare expression measures, which was computed with MAS and RMA. > > But I noticed that the expression-values are very different. > > e.g.: Expt1_R1.CEL: Gen: 1007_s_at > > RMA: 8,06941 > > MAS: 236,16853028 > > 1. How can I interpret this difference? RMA returns log2 transformed data, so you either have to take the logarithm for your MAS data, or 'unlog' the RMA data. Jim > 2. And which mathematical methods for comparison between preprocessing can I use? > > thanks, > Mohammad Esad-Djou > > Interdisciplinary Centre for Bioinformatics > Leipzig, Germany > > > ____________________________________________________________________ ______ > Erweitern Sie FreeMail zu einem noch leistungsstarkeren E-Mail- Postfach! > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.