[BioC] DESeq diagnostics
anders at embl.de
Tue Oct 9 22:12:21 CEST 2012
On 07/10/12 18:17, Michael wrote:
> BTW, is it better to estimate dispersion in paires (treatment1 / control;
> treatment2 / control, ...) or rather for a whole dataset in case of 1
> control / treatment 1-6 (each sample in 2 biol rep).
As you have only two replicates per treatment, you are most likely
better of if you use your whole data set to get reasonably precise
However, if there is one treatment where the replicates show stronger
differences than in the othe treatments, this will increase dispersion
and hence reduce power for all comparisons. So, better double-check that
this is not the case, e.g. with the plotPCA function.
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