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Old 01-10-2014, 05:39 AM   #1
Junior Member
Location: boston

Join Date: Jun 2010
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Default non balanced design in DESeq2

I apologize in advance if this question has been already asked but I`m wondering if DESeq2 can handle a non factorial design. Let`s say I have 2 factors A and B, A has 2 levels and B has 3. Each of the 2 levels of A is treated with each level of B, except 2 samples where only one level of B could be recovered. One option is obviously to exclude those 2 samples, but I was wondering if there is a way to include them in the analysis and increase the sample size.
Thank you in advance!

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Old 01-10-2014, 06:10 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

You can do incomplete factorial designs with DESeq (or edgeR or limma).
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