[BioC] Random effect for RNAseq data in Limma package

Gordon K Smyth smyth at wehi.EDU.AU
Sun Nov 10 11:37:28 CET 2013

Dear Fabina,

The same instructions apply exactly the same for RNA-seq as for 
microarrays.  (This is one of the advantages of voom.)

Best wishes

> Date: Thu, 7 Nov 2013 16:47:23 +0100
> From: sci yasmin <sci.yasmin at gmail.com>
> To: bioconductor at r-project.org
> Subject: [BioC] Random effect for RNAseq data in Limma package
> Dear bioconducter mailing list
> I am a PhD student in plant breeding department in Norway. I am using 
> your limma package for analyzing my RNA-seq data. Since I am not a 
> statistician, so I am asking you a very small question from you. I have 
> a 2 factorial experiment with a split plot design, where block was the 
> main plot and lane was in sub plot. Now I want to fit the block as fixed 
> effect and lane as a random effect. Could you please kindly tell me very 
> briefly that how can I define fixed and random effect together in limma 
> package? I read section 9.7 and 11.3 where it was described for 
> microarray data but dont know how to handel with voom function for 
> RNAseq data.
> Best wishes
> Fabina
> Oslo, Norway

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