Question: Fwd: edgeR dispersions
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gravatar for Bogdan
7.4 years ago by
Bogdan580
Palo Alto, CA, USA
Bogdan580 wrote:
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]]
edger • 1.6k views
ADD COMMENTlink modified 7.4 years ago by alessandro.guffanti@genomnia.com330 • written 7.4 years ago by Bogdan580
Answer: Fwd: edgeR dispersions
0
gravatar for alessandro.guffanti@genomnia.com
7.4 years ago by
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@gmail.com> To: <bioconductor@stat.math.ethz.ch> 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@r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor [https://stat.ethz.ch/mailman/listinfo/bioconductor] Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [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 è da considerarsi vietato ed abusivo. The information transmitted is intended only for the per...{{dropped:10}}
ADD COMMENTlink written 7.4 years ago by alessandro.guffanti@genomnia.com330
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@genomnia.com> 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@gmail.com> > To: <bioconductor@stat.math.ethz.ch> > 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@r-project.org > 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 è da > considerarsi vietato ed abusivo. > > The information transmitted is intended only for the p...{{dropped:15}}
ADD REPLYlink written 7.4 years ago by Bogdan580
I see your point .. try to set up manually the common dispersion to 0 or any reasonable value then. I see it is set up automatically to NA HTH A ----------------------------------------------------- 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@gmail.com> To: Guffanti Alessandro <alessandro.guffanti@genomnia.com> Cc: bioconductor@stat.math.ethz.ch Date: Sat, 7 Jul 2012 00:07:19 -0700 Subject: Re: [BioC] Fwd: edgeR dispersions 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@genomnia.com [mailto:alessandro.guffanti@genomnia.com]=""> 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 [tel:%2B39-0293305.702] Fax: +39-0293305.777 [tel:%2B39-0293305.777] http://www.genomnia.com [http://www.genomnia.com/] "If you can dream it, you can do it" (Walt Disney) -----Original Message----- From: Bogdan Tanasa <tanasa@gmail.com [mailto:tanasa@gmail.com]=""> To: <bioconductor@stat.math.ethz.ch [mailto:bioconductor@stat.math.ethz.ch]=""> 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 [http://de.com/] <- exactTest(d) Error in if (any(dispersion < 0)) stop("dispersion must be non- negative") : missing value where TRUE/FALSE needed > de.com [http://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@r-project.org [mailto:Bioconductor@r-project.org] https://stat.ethz.ch/mailman/listinfo/bioconductor [https://stat.ethz.ch/mailman/listinfo/bioconductor] Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor [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 è da considerarsi vietato ed abusivo. The information transmitted is intended only for the pe...{{dropped:28}}
ADD REPLYlink written 7.4 years ago by alessandro.guffanti@genomnia.com330
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 at imls.uzh.ch 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 at genomnia.com> 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 at="" gmail.com=""> >> To: <bioconductor at="" stat.math.ethz.ch=""> >> 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 at r-project.org >> 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 ? da >> considerarsi vietato ed abusivo. >> >> The information transmitted is intended only for the p...{{dropped:15}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 7.4 years ago by Mark Robinson870
Thanks, gentlemen. I am just going to follow Mark's suggestion in the manual and set up the dispersion to 0.4. happy weekend ! On Sat, Jul 7, 2012 at 12:32 PM, Mark Robinson <mark.robinson@imls.uzh.ch>wrote: > > 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/in st/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@imls.uzh.ch > 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@genomnia.com> 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@gmail.com> > >> To: <bioconductor@stat.math.ethz.ch> > >> 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@r-project.org > >> 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 è da > >> considerarsi vietato ed abusivo. > >> > >> The information transmitted is intended only for the p...{{dropped:15}} > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
ADD REPLYlink written 7.4 years ago by Bogdan580
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