Technical Replicates and RUVs Normalisation
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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 and in the tutorial .

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


rnaseq ruvnormalize normalization technical replicates • 1.3k views

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