Thanks a lot Michael,
Thats a great help.
Best wishes,
Suparna
Dr. Suparna Mitra
Department of Molecular and Clinical Pharmacology
Institute of Translational Medicine University of Liverpool
Block A: Waterhouse Buildings
1-5 Brownlow Street
Liverpool
L69 3GL
Tel. +44 (0)151 795 5414
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On 27 January 2014 21:18, Michael Love <michaelisaiahl...@gmail.com> wrote:
> hi Suparna,
>
> CountDataSet is the class used in DESeq, while DESeqDataSet is the class
> used in DESeq2.
>
> You can convert a CountDataSet to a DESeqDataSet using the steps outlined
> in the vignette, "1.2.3 Count matrix input".
>
> Mike
>
>
>
>
> On Sun, Jan 26, 2014 at 11:28 PM, Suparna Mitra <
> suparna.mitra...@gmail.com> wrote:
>
>> Hi All,
>> I am having a problem while running getVarianceStabilizedData in DDSeq2
>> package.
>>
>> data.vsd<-getVarianceStabilizedData(data)
>> Error in (function (classes, fdef, mtable) :
>> unable to find an inherited method for function dispersionFunction for
>> signature "CountDataSet"
>>
>> Though the function looks okay
>> > dispersionFunction
>> standardGeneric for "dispersionFunction" defined from package "DESeq2"
>>
>> function (object)
>> standardGeneric("dispersionFunction")
>> <environment: 0x7fe7a9c5d140>
>> Methods may be defined for arguments: object
>> Use showMethods("dispersionFunction") for currently available ones.
>>
>> Can anybody please help?
>> Thanks,
>> Mitra.
>>
>> [[alternative HTML version deleted]]
>>
>>
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>>
>
>
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