[BioC] DESeq estimateDispersions() problem

[Nicolas Delhomme]

Dear Karl,

Can you please paste in your session info as well, that will help the maintainer.

To get it use the sessionInfo command in R after having loaded the DESeq package.

I would not expect such a function to disappear without being deprecated, but you can always lookup the package recent changes using the news command:

news(package="DESeq")

Depending on your R version, you can query more specific new, i.e. if you're using the current development version:

news(Version >= "1.9", package="DESeq")

As I said, since I do not expect such a drastic change in the DESeq API, make sure as well that nothing changed in your R environment: check that no previous session is restored when you start R (look for an .Rdata file in the startup directory), etc.

Cheers,

---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------





On May 31, 2012, at 2:29 PM, Karl Lundén wrote:

> Dear all,
> I can not get the DESeq function estimateDispersions() to function as it usually
> does. Have there been any recent updates in DESeq or in R that explains why
> estimateDispersions doesn't work? I use R on a grid engine and everything worked
> fine earlier this spring.
> Thanks
> Karl 
> ================================================
>> library(DESeq)
>> ?newCountDataSet()
>> library(DESeq)
>> ?estimateDispersions()
> Error in .helpForCall(topicExpr, parent.frame()) : 
>  no methods for 'estimateDispersions' and no documentation for it as a function
>> estimateDispersions()
> Error: could not find function "estimateDispersions"
> 
> ## Other functions do work
>> newCountDataSet()
> Error in as.matrix(countData) : 
>  argument "countData" is missing, with no default
> 
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