On Tue, 22 Jul 2003 bioconductor-r > Send Bioconductor mailing list submissions to > bioconductor@stat.math.ethz.ch > > To subscribe or unsubscribe via the World Wide Web, visit > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > or, via email, send a message with subject or body 'help' to > bioconductor-request@stat.math.ethz.ch > > You can reach the person managing the list at > bioconductor-owner@stat.math.ethz.ch > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bioconductor digest..." > > > Today's Topics: > > 1. implementation of an add-on package (Stephen Moore) > 2. RNA degradation plot (Bill Kenworthy) > 3. R Hangs (michael watson (IAH-C)) > 4. Affy digestion plots (Oliver Hartmann) > > > ---------------------------------------------------------------------- > Using the affy library, I did an RNA degradation plot for 5 mu74Av2 > mouse chips and it generated the figures below. I do not have anything > to measure this against - if someone has some figures on what "degraded" > RNA looks like (and/or some thresholds), and a representative plot I > would be appreciative. > > slope -0.0201 -0.236 -0.228 -0.0884 -0.209 > pvalue 0.858 0.0517 0.0751 0.44 0.115 > > Thanks > BillK I used mainly HGU95a chips in developing the method. for that chiptype, 232 very high quality chips had slopes between .05 and .3 Comparison of other hgu95a chips to the 3'/5' housekeeping ratios suggest that slopes close to 1 (.75 to 1.05) are borderline, whereas slopes larger than 1.1 seem to indicate very bad quality rna. slope does not appear to be a linear measure of RNA quality. This is based on small sample though and does not yet consititute a rule. We hope to have large sample validation coming soon. I would say that your mouse chips here look great. The one large hgu133 experiment I looked at had slopes much higher than 1, although 3'/5' ratios were all good. I don't know what to say about that chipset yet. chips a and b were similar though. Leslie Cope > -------------------------