[BioC] Single nucleotide based RNAseq normalization with edgeR

[Gordon K Smyth]

Hi Jens,

I don't know what you mean by single nucleotide based normalization, 
however the following comments may be helpful.

edgeR automatically adjusts for library sizes, whether you include an 
explicit normalization step or not.  Normalization is a separate issue, 
and is intended to deal with more subtle issues.

Normalization, as edgeR does it, does not require replicates.

Best wishes
Gordon

> Date: Fri, 04 Feb 2011 11:28:15 +0100
> From: Jens Georg <jens.georg at biologie.uni-freiburg.de>
> To: bioconductor at r-project.org
> Subject: [BioC] Single nucleotide based RNAseq normalization with
> 	edgeR?
> Message-ID: <4D4BD4BF.4010009 at biologie.uni-freiburg.de>
> Content-Type: text/plain; charset=ISO-8859-15; format=flowed
>
>
>
> Dear edgeR users and developers,
>
> we used Solexa sequencing in order to detect RNase E processing sites.
> Therefor we splitted a RNA sample and treated one half with RNase E
> prior to cDNA synthesis and sequencing. The libraries differ in size
> (1.918.953 and 1.208.586 reads respectively) which clearly necessitates
> a normalization step. Furthermore we expect site specific differences
> rather than differences in the accumulation of the full length RNAs.
>
> So I want to ask, if it is appropiate to do a single nucleotide based
> normalization with edgeR and do you think a reliable basic normalization
> is possible without replicates?
>
> Thank you for your comments.
>
> Best regards
>
> Jens

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