edgeR: mixing technical replicates from Illumina HiSeq and MiSeq

Hi,

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:

https://stat.ethz.ch/pipermail/bioconductor/2010-April/033099.html

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!
Nick

	[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor