mark.robinson at imls.uzh.ch
Tue Aug 9 23:35:55 CEST 2011
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,
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:
> An object of class "DGEList"
> files lib.size norm.factors
> allcontrol allcontrol.txt 318020 1
> allstress allstress.txt 306479 1
> 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
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