7 Jul 2012 21:32
Re: edgeR dispersions
Hi Bogdan, > thanks for your email : it was possible to use edgeR in the past (previous > versions) with no replicates, > (so of course there is no dispersion), but edgeR worked ..while now I am > getting errors ... thanks, The default has changed to make users make a conscious decision of what to do about having no replicates. The previous default (setting dispersion to a low value) was probably not ideal. As Alessandro says, read the "What to do if you have no replicates" section of the user's guide: http://www.bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf Best, Mark ---------- Prof. Dr. Mark Robinson Bioinformatics Institute of Molecular Life Sciences University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland v: +41 44 635 4848 f: +41 44 635 6898 e: mark.robinson@... o: Y11-J-16 w: http://tiny.cc/mrobin ---------- http://www.fgcz.ch/Bioconductor2012 On 07.07.2012, at 09:07, Bogdan Tanasa wrote: > Hi Alessandro, > > thanks for your email : it was possible to use edgeR in the past (previous > versions) with no replicates, > (so of course there is no dispersion), but edgeR worked ..while now I am > getting errors ... thanks, > > Bogdan > > > > > On Sat, Jul 7, 2012 at 12:02 AM, Guffanti Alessandro < > alessandro.guffanti@...> wrote: > >> Hi Bogdan - you answered by yourself: you don't have replicates, so how >> can any software estimate any kind of (common or tagwise) dispersion ? >> there is one section on edgeR manual with interesting hints about what you >> can - and can not - evaluate with such 'minimal' experiments >> >> My two cents, regards, >> >> Alessandro >> ----------------------------------------------------- >> *Alessandro Guffanti - Bioinformatics, Genomnia srl* >> Via Nerviano, 31 - 20020 Lainate, Milano, Italy >> Ph: +39-0293305.702 Fax: +39-0293305.777 >> http://www.genomnia.com >> "If you can dream it, you can do it" (Walt Disney) >> >> -----Original Message----- >> From: Bogdan Tanasa <tanasa@...> >> To: <bioconductor@...> >> Date: Fri, 6 Jul 2012 15:57:13 -0700 >> Subject: [BioC] Fwd: edgeR dispersions >> >> Dear all, >> >> I would appreciate a suggestion about edgeR : I have a GRO-seq dataset (CTL >> vs TREAT, no replicates, just 1 sample for CTL and 1 sample for TREAT >> condition), >> and I am assessing the differential expression by using edgeR, but I am >> getting an error : any suggestion would be appreciated. thanks very much ! >> >>> d <- estimateCommonDisp(d) >> Warning message: >> In estimateCommonDisp(d) : >> There is no replication, setting dispersion to NA. >> >>> de.com <- exactTest(d) >> Error in if (any(dispersion < 0)) stop("dispersion must be non-negative") : >> missing value where TRUE/FALSE needed >> >>> de.com <- exactTest(d,dispersion=0) >> Error in binomTest(s1[pois], s2[pois], p = n1/(n1 + n2)) : >> y1 and y2 must be non-negative >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@... >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> ----------------------------------------------------------- >> Il Contenuto del presente messaggio potrebbe contenere informazioni >> confidenziali a favore dei >> soli destinatari del messaggio stesso. Qualora riceviate per errore questo >> messaggio siete pregati >> di cancellarlo dalla memoria del computer e di contattare i numeri sopra >> indicati. Ogni utilizzo o >> ritrasmissione dei contenuti del messaggio da parte di soggetti diversi >> dai destinatari รจ da >> considerarsi vietato ed abusivo. >> >> The information transmitted is intended only for the p...{{dropped:15}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor _______________________________________________ Bioconductor mailing list Bioconductor@... https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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