[BioC] edgeR DGEList

[Mark Robinson]

Hi Jahn,

I've cc'd the list.  Look, a lot of people say that you must must must have raw counts for this and strictly, this is true.  My view is that as long as there are not too too many ambiguous reads, then this portioning off of reads in a non-integer fashion to features will not create such a huge violation of the edgeR modeling assumptions.  I could be wrong though, as I have not studied it in any depth.  After all, all models are wrong, some are useful.

Best, Mark

----------
Prof. Dr. Mark Robinson
Bioinformatics, Institute of Molecular Life Sciences
University of Zurich
http://ow.ly/riRea






On 12.12.2013, at 14:55, Jahn Davik <jahn.davik at bioforsk.no> wrote:

> Mark,
> I intended to ask you this one:
> I have been using Trinity and Trinity uses RSEM to generate the counts matrix -  a counts matrix I hoped could be used for downstream analyses in edgeR.  However, RSEM gives counts-data that not necessarily are integers and provided I get this right, the reason for is  that RSEM takes into account multiply mapped reads, read mapping uncertainty, other bias corrections, etc. 
> 
> So, my question is simply: Would it be wrong to use these counts data in edgeR?
> 
> Best regards,
> Jahn
> 
> 
> xxxxxxxxxxxxxxxxxx
> Dr  Jahn Davik
> Bioforsk
> Kvithamar
> N-7512 Stjordal
> Norway
> 
> cell: (+47) 979 54 473
> switch: +47 4060 4100
> sentralbord: 03246
> skype: jahn.davik
> 
> 
> 
> 
> 
> 
> 
> 
> -----Opprinnelig melding-----
> Fra: Mark Robinson [mailto:mark.robinson at imls.uzh.ch] 
> Sendt: 12. desember 2013 09:57
> Til: Jahn Davik [guest]
> Kopi: bioconductor at r-project.org; Jahn Davik
> Emne: Re: [BioC] edgeR DGEList
> 
> Jahn:  Load the package first .
> 
> library("edgeR")
> dge <- DGEList(counts=cots)
> .
> 
> Best, Mark
> 
> 
> On 12.12.2013, at 09:35, Jahn Davik [guest] <guest at bioconductor.org> wrote:
> 
>> 
>> Hi there,
>> I am trying to import the counts data (='cots', count data set 
>> generated in Trinity) into R. When I run $ dge<-DGEList(counts=cots), I get the reply:
>> 
>> Error: could not find 'DGEList'
>> 
>> BTW: I start the session by
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("edgeR")
>> biocLite("DESeq")
>> 
>> Probably trivial, but help is still greatly appreciated.
>> Thanks.
>> 
>> jahn
>> 
>> 
>> 
>> 
>> -- output of sessionInfo(): 
>> 
>> Error: could not find 'DGEList'
>> 
>> --
>> Sent via the guest posting facility at bioconductor.org.
>> 
>> _______________________________________________
>> 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
>