expression call

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Glazko, Galina ▴ 350

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ADD COMMENT • link updated 18.2 years ago by James W. MacDonald 67k • written 18.2 years ago by Glazko, Galina ▴ 350

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James W. MacDonald 67k

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Hi Galina, Glazko, Galina wrote: > Dear list > > > > I need to select genes which are actually expressed in a set of Affy > chips. > > I've heard about 'expression call' thing, but I do not know exactly > whether it is relevant to my problem. I think you mean 'present call', which measures whether or not the intensities of PM probes for a particular probeset are significantly different from the corresponding MM probes. This is based on the idea that MM probes measure background binding, so if the PM probes are different, the transcript is assumed to be present (or expressed). You can get these values by using the mas5calls() function in the affy package. See ?mas5calls for more information. Best, Jim > > Would someone help me to solve it? > > > > Best regards > > Galina > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC 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.

ADD COMMENT • link 18.2 years ago James W. MacDonald 67k

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On Tuesday 22 August 2006 20:24, James W. MacDonald wrote: > Hi Galina, > > Glazko, Galina wrote: > > Dear list > > > > > > > > I need to select genes which are actually expressed in a set of Affy > > chips. > > > > I've heard about 'expression call' thing, but I do not know exactly > > whether it is relevant to my problem. > > I think you mean 'present call', which measures whether or not the > intensities of PM probes for a particular probeset are significantly > different from the corresponding MM probes. This is based on the idea > that MM probes measure background binding, so if the PM probes are > different, the transcript is assumed to be present (or expressed). > > You can get these values by using the mas5calls() function in the affy > package. See ?mas5calls for more information. Hi, how would one get presence or absence calls with gcrma normalized data? Is normalizing it with gcrma and then adding the mas5calls the most sensible or only way to do it? Or is there a know cutoff for gcrma normalized data where people have measured with RT-PCR that a transcript is actually not expressed? thank you very much, Ido

ADD REPLY • link 18.2 years ago Ido M. Tamir ▴ 320

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Hi Ido, The presence/absence calls are calculated from the raw PM and MM probes and is done independently from whatever pre-processing suite you decide to use. mas5calls() works on an AffyBatch object, so the calls will the same regardless of whether you use gcrma(), rma() mas5(), or any combination of the options in expresso() to process your probe-level data (AffyBatch object) into one value per probeset (exprSet object). Cheers, Jenny >Hi, > >how would one get presence or absence calls with gcrma normalized data? >Is normalizing it with gcrma and then adding the mas5calls the most >sensible or only way to do it? > >Or is there a know cutoff for gcrma normalized data where people >have measured with RT-PCR that a transcript is actually not expressed? > >thank you very much, >Ido > >_______________________________________________ >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 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

ADD REPLY • link 18.2 years ago Jenny Drnevich ★ 2.2k

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