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

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