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/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@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]]
> >>
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> >>
> >>
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