[Bioc-sig-seq] edgeR/454

[Mark Robinson]

Hi Estefania,

In your $samples data.frame, you don't have a "group" variable listed (it doesn't recognize "files").  Perhaps you made this yourself instead of using the DGEList() constructor?

You could reconstruct this with:

RG1 <- DGEList(counts=RG$counts, group=c("allcontrol","allstress"))
d <- estimateCommonDisp(RG)

Hope that helps,
Mark

On Aug 10, 2011, at 5:51 AM, Estefania Mancini wrote:

> Dear All
> I am trying to analyse 2 454 RNA-seq dataset.
> I have only 2 condition, control and stress-
> It is possible to use edgeR? I have prepared the file with the columns tags->reads.
> I can load the files and build the "object of class "DGEList", which looks like this:
> 
>> RG
> An object of class "DGEList"
> $samples
>                    files lib.size norm.factors
> allcontrol allcontrol.txt   318020            1
> allstress   allstress.txt   306479            1
> 
> $counts
>                allcontrol allstress 
> Gen11900.1      50872     51431      
> Gen12050.1      39874     40052       
> Gen24780.1      33951     32149       
> Gen12070.1      26733     29256       
> Gen11930.1      23858     28396       
> 18213 more rows ...
> 
> but when I try to apply:
>> d = estimateCommonDisp(RG)
> I have the following error:
> Error in `$<-.data.frame`(`*tmp*`, "group", value = integer(0)) : 
>  replacement has 0 rows, data has 2
> 
> So I cannot continue analysing the data.
> Any suggestion will be helpful
> Thanks in advance
> Estefania
> 
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