DESeq estimateDispersions
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Lucia Peixoto ▴ 330
@lucia-peixoto-4203
Last seen 9.6 years ago
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]]
Coverage DESeq Coverage DESeq • 3.8k views
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@mikelove
Last seen 11 hours ago
United States
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]]
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Simon Anders ★ 3.7k
@simon-anders-3855
Last seen 3.7 years ago
Zentrum für Molekularbiologie, Universi…
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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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 > > > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.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=""> > -- 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]]
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