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Old 01-11-2018, 01:51 PM   #2
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Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438

You may want to just split the data up into per-stimulation chunks. Otherwise the modeling in DESeq2 will use all samples and all stimulations to establish dispersions. If the separate stimulations are meant to be experimentally separate then you should not put all of the into the same model. So you'll run 'DESeqDataSetFromHTSeqCount' 100 times each with a subset of your data corresponding to a single stimulation.
/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
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