[BioC] deseq for multiple groups with no replicate

[Wolfgang Huber]

Dear Yolande

did you note the error message and have you checked whether there are NA 
or other non-numeric values in your dataset?

	Wolfgang

Il Apr/13/11 2:31 AM, Yolande Tra ha scritto:
> Hi Simon,
>
> I have tried clustering the proteins, first I transposed the data and
> applied the minimal set of commands but could not go further. Here is my
> code and the error message.
>
> tspectral=t(spectral)
> cds2=newCountDataSet(tspectral,rep( "dummy", ncol(tspectral)))
>> cds2
> CountDataSet (storageMode: environment)
> assayData: 5 features, 36 samples
>    element names: counts
> protocolData: none
> phenoData
>    sampleNames: Gene_01 Gene_02 Gene_03 Gene_04 ... Gene_36 (36
>      total)
>    varLabels: sizeFactor condition
>    varMetadata: labelDescription
> featureData: none
> experimentData: use 'experimentData(object)'
> Annotation:
>> cds2=estimateSizeFactors(cds2)
>> cds2=estimateVarianceFunctions(cds2)
> Error in estimateVarianceFunctions(cds2) :
>    NAs found in size factors. Have you called already 'estimateSizeFactors'?
>
> Thank you for your help,
> Yolande
> On Tue, Apr 5, 2011 at 5:22 AM, Simon Anders<anders at embl.de>  wrote:
>
>> Hi Yolanda
>>
>>
>> On 04/04/2011 07:34 PM, Yolande Tra wrote:
>>
>>> For clustering the proteins what would be conds (defined in the
>>> vignette) in
>>> cds3<-newCountdataSet(countsTable,conds)
>>> since there are many proteins with no specific condition.
>>>
>>
>> Just put something, e.g.,
>>
>>    cds3<- newCountDataSet( countsTable,
>>       rep( "dummy", ncol(countsTable) )
>>
>> This assigns the same condition to all of them. Of course, you cannot use
>> the 'nbinomTest' function, if you have only one condition, but that wouldn't
>> make sense anyway.
>>
>>
>> In the vignette there were two conditions: "N" and "T".
>>> For three different people (not 40), how you would define the cds in the
>>> command
>>> res<=nbinom(cds,"N","T").
>>>
>>
>> In a contrast, you compare two condition. In the vignette example, we ask:
>> Is the expression in "T" stronger or weaker than in "N"?
>>
>> How would you generalize such a question to three conditions? I don't see
>> what other option there is than to make three pair-wise comparisons --
>> unless you want to go away from the "which condition has the stronger
>> expression?" kind of question to some other hypothesis formulation.
>>
>>   Simon
>>
>>
>>
>
> 	[[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

-- 


Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber