[Bioc-sig-seq] edgeR/454

Estefania Mancini estefania.mancini at indear.com
Tue Aug 9 21:51:40 CEST 2011

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"
                    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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