Technical Replicates and RUVs Normalisation
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@thomaswolfe-9344
Last seen 6.5 years ago

Dear all,

I am working with 19 RNAseq sample, 10 of which have 2 technical replicates (same individuals in a population).

I am trying to correct for a clear batch effect using the RUVs approach as described in http://nar.oxfordjournals.org/content/early/2015/07/21/nar.gkv736.full and in the tutorial https://github.com/drisso/peixoto2015_tutorial/blob/master/Peixoto_Additional_File_1.Rmd .

How should I combine these technical replicates after normalisation to avoid pseudo-replication when I do the differential expression part?

Do the factors of unwanted variance, found after RUVs, already take into account the unbalance in the replication design? If not, is there a way to include this info in the glm design given to EdgeR (or DEseq) when we do the DE analysis.

Thank you for your help

Thomas

rnaseq ruvnormalize normalization technical replicates • 1.3k views
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