Hi,
I am trying to run DESeq and I keep getting the following error after
trying estimateDispersions
Error in parametricDispersionFit(means, disps) :
Parametric dispersion fit failed. Try a local fit and/or a pooled
estimation. (See '?estimateDispersions')
I cannot figure out why this is happening, I have 4 control and 4 case
samples
the code immediately preceding the error looks like this;
conds=rep(0,ncol(C))
cds <- newCountDataSet( C, conds )
cds <- estimateSizeFactors( cds )
cds <- estimateDispersions( cds )
where C is my coverage matrix
The matrix does have 355042 rows, is that a problem?
thanks for the help
PS: This is not "traditional" RNA-seq data, each row is a window in
the
genome and the values on the matrix are mapped reads in each sample
for
each window
--
Lucia Peixoto PhD
Postdoctoral Research Fellow
Laboratory of Dr. Ted Abel
Department of Biology
School of Arts and Sciences
University of Pennsylvania
"Think boldly, don't be afraid of making mistakes, don't miss small
details, keep your eyes open, and be modest in everything except your
aims."
Albert Szent-Gyorgyi
[[alternative HTML version deleted]]
hi Lucia,
On Wed, Apr 17, 2013 at 5:32 PM, Lucia Peixoto <luciap@iscb.org>
wrote:
> Hi,
>
> I am trying to run DESeq and I keep getting the following error
after
> trying estimateDispersions
>
> Error in parametricDispersionFit(means, disps) :
> Parametric dispersion fit failed. Try a local fit and/or a pooled
> estimation. (See '?estimateDispersions')
>
>
> I cannot figure out why this is happening, I have 4 control and 4
case
> samples
> the code immediately preceding the error looks like this;
> conds=rep(0,ncol(C))
> cds <- newCountDataSet( C, conds )
> cds <- estimateSizeFactors( cds )
> cds <- estimateDispersions( cds )
>
>
You have set all the conditions equal to zero. This should instead be
a
factor which gives the condition of the samples. See the description
of
this in ?newCountDataSet.
If you continue to get the error, follow the instructions in the
message,
i.e. read the help for ?estimateDispersions and try using the argument
fitType="local"
> where C is my coverage matrix
> The matrix does have 355042 rows, is that a problem?
>
>
The number of rows is not a problem.
Mike
[[alternative HTML version deleted]]
Hi
On 17/04/13 17:32, Lucia Peixoto wrote:
> Error in parametricDispersionFit(means, disps) :
> Parametric dispersion fit failed. Try a local fit and/or a pooled
> estimation. (See '?estimateDispersions')
[...]
> PS: This is not "traditional" RNA-seq data, each row is a window in
the
> genome and the values on the matrix are mapped reads in each sample
for
> each window
The parametric fit fails sometimes, especially on non-standard data
sets. This is why we offer the local fit as a fall-back.
Simon
HI All,
thanks very much for the help, doing local fit fixes the issue
I a not sure I understand what is the impact of doing this in terms of
the
accuracy of the estimates
can someone explain?
will it affect greatly the number of differential calls at a
particular
cutoff?
thanks
Lucia
On Wed, Apr 17, 2013 at 1:41 PM, Simon Anders <anders@embl.de> wrote:
> Hi
>
>
> On 17/04/13 17:32, Lucia Peixoto wrote:
>
>> Error in parametricDispersionFit(means, disps) :
>> Parametric dispersion fit failed. Try a local fit and/or a
pooled
>> estimation. (See '?estimateDispersions')
>>
> [...]
>
> PS: This is not "traditional" RNA-seq data, each row is a window in
the
>> genome and the values on the matrix are mapped reads in each sample
for
>> each window
>>
>
> The parametric fit fails sometimes, especially on non-standard data
sets.
> This is why we offer the local fit as a fall-back.
>
> Simon
>
>
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>
--
Lucia Peixoto PhD
Postdoctoral Research Fellow
Laboratory of Dr. Ted Abel
Department of Biology
School of Arts and Sciences
University of Pennsylvania
"Think boldly, don't be afraid of making mistakes, don't miss small
details, keep your eyes open, and be modest in everything except your
aims."
Albert Szent-Gyorgyi
[[alternative HTML version deleted]]
