Hi Mark,

I have two samples "Y" and "S" (with no replicates), and following edgeR
manual on "what to do if you do not have replicates", I am getting the
following results below. The end message is "No residual df: cannot
estimate dispersion". Please could you let me know what is going wrong ..
Thanks a lot !

>raw.data <- read.delim("file")
>d <- raw.data[,2:3]
>rownames(d) <- raw.data[,1]

> group <- factor(c("Y","S"))
> design <- model.matrix(~group)
>d <- DGEList(counts = d, group=group)
Calculating library sizes from column totals.
> dim(d)
[1] 4013    2
> d <- calcNormFactors(d)
> d
An object of class "DGEList"
$samples
  group lib.size norm.factors
Y     Y   628062     1.049011
S     S   422542     0.953279

$counts
                         Y   S
chr8:53670099-53691880 132 109
chr8:71033673-71122126 221 107
chr8:74069636-74074658   7   1
chr6:72172478-72187779 203 114
chr6:72096548-72115900  36  15
4008 more rows ...

$all.zeros
chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658
                 FALSE                  FALSE                  FALSE
chr6:72172478-72187779 chr6:72096548-72115900
                 FALSE                  FALSE
4008 more elements ...

>
d<-estimateGLMCommonDisp(d,design,method="deviance",robust="TRUE",subset=NULL)
Warning message:
In estimateGLMCommonDisp.default(y = y$counts, design = design,  :
  No residual df: cannot estimate dispersion

For Common Dispersion (no GLM modeling):

> d<-estimateCommonDisp(d,design)
Warning message:
In estimateCommonDisp(d, design) :
  There is no replication.  Setting common dispersion to 0.
> d
An object of class "DGEList"
$samples
  group lib.size norm.factors
Y     Y   628062     1.049011
S     S   422542     0.953279

$counts
                         Y   S
chr8:53670099-53691880 132 109
chr8:71033673-71122126 221 107
chr8:74069636-74074658   7   1
chr6:72172478-72187779 203 114
chr6:72096548-72115900  36  15
4008 more rows ...

$all.zeros
chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658
                 FALSE                  FALSE                  FALSE
chr6:72172478-72187779 chr6:72096548-72115900
                 FALSE                  FALSE
4008 more elements ...

$common.dispersion
[1] 1e-16

$pseudo.alt
                                Y         S
chr8:53670099-53691880 103.192083 139.42506
chr8:71033673-71122126 172.781586 136.86720
chr8:74069636-74074658   5.453794   1.30187
chr6:72172478-72187779 158.707305 145.81970
chr6:72096548-72115900  28.129216  19.20588
4008 more rows ...

$conc
$conc.common
chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658
          2.270073e-04           3.089534e-04           7.535477e-06
chr6:72172478-72187779 chr6:72096548-72115900
          2.985930e-04           4.803864e-05
4008 more elements ...

$conc.group
                                  S            Y
chr8:53670099-53691880 2.706055e-04 2.003510e-04
chr8:71033673-71122126 2.656403e-04 3.354361e-04
chr8:74069636-74074658 2.482619e-06 1.062467e-05
chr6:72172478-72187779 2.830186e-04 3.081155e-04
chr6:72096548-72115900 3.723929e-05 5.464117e-05
4008 more rows ...


$common.lib.size
$pseudo
                                Y         S
chr8:53670099-53691880 103.192083 139.42506
chr8:71033673-71122126 172.781586 136.86720
chr8:74069636-74074658   5.453794   1.30187
chr6:72172478-72187779 158.707305 145.81970
chr6:72096548-72115900  28.129216  19.20588
4008 more rows ...

$conc
$conc.common
chr8:53670099-53691880 chr8:71033673-71122126 chr8:74069636-74074658
          2.270073e-04           3.089534e-04           7.535477e-06
chr6:72172478-72187779 chr6:72096548-72115900
          2.985930e-04           4.803864e-05
4008 more elements ...

$conc.group
                                  S            Y
chr8:53670099-53691880 2.706055e-04 2.003510e-04
chr8:71033673-71122126 2.656403e-04 3.354361e-04
chr8:74069636-74074658 2.482619e-06 1.062467e-05
chr6:72172478-72187779 2.830186e-04 3.081155e-04
chr6:72096548-72115900 3.723929e-05 5.464117e-05
4008 more rows ...


$N
[1] 515153


On Fri, Nov 18, 2011 at 12:39 PM, Mark Robinson
<mark.robinson@imls.uzh.ch>wrote:

>
>
> On 18.11.2011, at 21:27, Bogdan Tanasa wrote:
>
> > Dear all,
> >
> > are the functions "estimateGLMCommonDisp" and "estimateGLMTagwiseDisp"
> > available in edgeR on any platform ? I am using it on Linux/Ubuntu and
> > apparently, these functiosn are not available.
>
>
> What version of R/edgeR are you using?  Perhaps you have an old version?
>  These functions have been around for awhile.  What does sessionInfo() give?
>
> Mark
>
>
>
> >
> > thanks,
> >
> > Bogdan
> >
> >       [[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
>
>

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