[BioC] edgeR: mixing technical replicates from Illumina HiSeq and MiSeq

Nick N feralmedic at gmail.com
Thu Aug 28 18:23:51 CEST 2014


I have a study where a fraction of the samples have been replicated on 2
Illumina platforms (HiSeq and Miseq). These are technical replicates - the
library preparation is the same using the same biological replicates - it's
only the sequencing which is different.

My hunch was that I shall introduce the platform as as an additional
(blocking) factor in the analysis. Than I stumbled upon this post:


It recommends pooling the replicates. The post seems to apply to a
different case ("pure" technical replicates, i.e. no differences in the
sequencing platform used) so I probably shall ignore it. But I still feel a
bit uncertain of the best way to treat the technical replicates. Can you,
please, advise me on this?

many thanks!

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