[BioC] edgeR - technical and biological replication

[Gordon K Smyth]

Dear Jakob,

Yes, pool the technical replicates. Unlike microarrays, there's no gain 
from keeping the tech reps separate, unless you have good evidence they 
show greater than Poisson variability.  You could fit common dispersion to 
the technical replicates to check this, if you feel the need.  (To do 
that, setup one grouping factor which takes the same level for each run of 
technical replicates.)

Best wishes
Gordon

> Date: Mon, 26 Apr 2010 15:32:25 +0200
> From: Jakob Hedegaard <Jakob.Hedegaard at agrsci.dk>
> To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Subject: [BioC] edgeR - technical and biological replication
>
> 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
>
>
> ###############################
> 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

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