non balanced design in DESeq2

libro.s · 01-10-2014, 05:39 AM

Hi,
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!

Silvia

dpryan · 01-10-2014, 06:10 AM

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

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01-10-2014, 05:39 AM	#1
libro.s Junior Member Location: boston Join Date: Jun 2010 Posts: 2	non balanced design in DESeq2 Hi, 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! Silvia

01-10-2014, 06:10 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	You can do incomplete factorial designs with DESeq (or edgeR or limma).