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

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