Hello everyone, I was wondering what are acceptable values for the slopes generated using summaryAffyRNAdeg in the affy package. I assume 0.0 would be the ideal, but what values would be considered 'of concern', or too high? Any thoughts from users of the RNA deg function? Thanks. -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth Drive London, Ontario, Canada, N6A 5K8 phone: (519) 663-3253 fax: (519) 663-3037 dcarter@robarts.ca http://www.lrgc.ca/

Hi, I believe the consensus on this is that it is more important to have samples with comparable slopes than it is to actually quantitatively assess the slope itself. I have worked with clinical samples that gave me rather steep curves but the data was very good. Its just good to see that you don't have any samples with curves that are way out of what the others are doing. Yours, Lawrence _______________________________ Lawrence-Paul Petalidis Ph.D Candidate Department of Pathology Division of Molecular Histopathology University of Cambridge _______________________________ -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of David Carter Sent: 08 June 2004 18:46 To: Bioconductor list serv Subject: [BioC] AffyRNAdeg slopes Hello everyone, I was wondering what are acceptable values for the slopes generated using summaryAffyRNAdeg in the affy package. I assume 0.0 would be the ideal, but what values would be considered 'of concern', or too high? Any thoughts from users of the RNA deg function? Thanks. -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth Drive London, Ontario, Canada, N6A 5K8 phone: (519) 663-3253 fax: (519) 663-3037 dcarter@robarts.ca http://www.lrgc.ca/ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Like expression values, I don't think there is a 'good' value for the slope. Of more concern is how the slopes compare within a given set of chips. If they are all relatively parallel, this indicates that the RNA degradation and/or in vitro transcription were relatively similar for all of the samples. Since you are only interested in comparisons within a given set of chips, this is much more critical than an absolute slope. Anyway, in my experience, large differences in slope are less critical than big differences between the density plots. I find that outliers on the density plot nearly always require a redo of the chip, whereas chips with very different slopes in the RNA degradation plot may be usable. HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> David Carter <dcarter@robarts.ca> 06/08/04 01:45PM >>> Hello everyone, I was wondering what are acceptable values for the slopes generated using summaryAffyRNAdeg in the affy package. I assume 0.0 would be the ideal, but what values would be considered 'of concern', or too high? Any thoughts from users of the RNA deg function? Thanks. -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth Drive London, Ontario, Canada, N6A 5K8 phone: (519) 663-3253 fax: (519) 663-3037 dcarter@robarts.ca http://www.lrgc.ca/ _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor