[BioC] edgeR and DESeq2: model design and estimation of dispersion

Iddo Ben-dov iddobe at ekmd.huji.ac.il
Thu Jun 12 15:51:51 CEST 2014


in both edgeR and DESeq2, estimation of dispersion precedes negative binomial GLM fitting.

my question is, can I use a design formula when estimating dispersion which is different from the formula used for GLM fitting? specifically, I would like to use a simplified design when estimating dispersion and a full design for GLM fitting.

my motivation for doing so is that with the full design estimation of dispersion is too demanding for my computer and time.

my dataset includes 400 mRNAseq profiles (~22,000 genes). there are 100 controls and 100 cases, and each was sampled twice - before and after intervention.

thus, the full design is:
 ~ group*intervention + individual:group (blocking factor)

as I mentioned, estimation of dispersion with the above design is not practical, and I thus would like to simplify to:
~ group*intervention

and introduce the 'individual' blocking factor only for NB GLM fitting.

is this statistically valid?

appreciate any help,

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