[BioC] DESeq2 Regularised Log for Clustering of Genes

Michael Love michaelisaiahlove at gmail.com
Sun May 11 05:39:53 CEST 2014


On Sat, May 10, 2014 at 9:00 PM, Dario Strbenac
<dstr7320 at uni.sydney.edu.au> wrote:
> Hello,
>
> Those are two good ideas for analysing profiles. We are aware that the majority of published clustering methods are designed for analysing profiles. However, biologists have told us that transcription factors usually appear at levels many times lower than the genes they cause the transcription of, leading us to explore clustering with absolute levels.
>
>> I would divide before transformation or subtract after transformation
>
> Only the subtraction after transformation would be possible, because dividing before would cause non-integer values, causing the creation of a DESeqDataSet to fail, wouldn't it ?
>

Yes. you can subtract afterward.

> --------------------------------------
> Dario Strbenac
> PhD Student
> University of Sydney
> Camperdown NSW 2050
> Australia
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