[BioC] edgeR - technical and biological replication

[Jakob Hedegaard]

Hi,
I have a RNA-Seq dataset produced on a Illumina GA and wonder how to account for both technical and biological replication using edgeR.
The dataset consist of 48 individual samples (time series with 4-6 biological replica per time point, 9 time points in total) which have been sequenced in three GA runs (3 technical replica) using 12-plex sequencing (4 lanes/run) - that is a total of 144 profiles representing 3 technical replica and 4-6 biological replica.
Simply adding the counts from the 3 tech rep forming 48 profiles would be a start point, but it would be more powerful to include the tech rep in the analysis as well...

Best regards,
Jakob


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R version 2.11.0 (2010-04-22) 
x86_64-pc-mingw32 

locale:
[1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252    LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C                   
[5] LC_TIME=Danish_Denmark.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] edgeR_1.6.0

loaded via a namespace (and not attached):
[1] limma_3.4.0  tools_2.11.0