[Bioc-sig-seq] edgeR/454

[Davis McCarthy]

Hi Estefania

One more thing: since you have no replicates among your samples you
might like to read Section 11 of the edgeR Users Guide "What to do if
you have no replicates", which has some ideas about how you might go
about accounting for biological variability when you cannot estimate
it in the usual way.

Best wishes

Davis


On 10 August 2011 07:35, Mark Robinson <mark.robinson at imls.uzh.ch> wrote:
> 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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>
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-- 
---------------------------------------------------------------------------
Davis J McCarthy
Research Technician
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052, Australia
dmccarthy at wehi.edu.au
http://www.wehi.edu.au