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Old 08-12-2014, 02:38 PM   #22
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Location: US

Join Date: Aug 2014
Posts: 2
Smile Some questions about DESeq and DESeq2

Hi Simon,

I have three questions about DESeq here(referring to "Differential expression analysis for sequence count data"):

1. You set up three assumptions, what is the basis of equation(3) and eqation(4)? How to explain them? If explain details with intuition and mathematics, that will be best. Thank you very much.

2. Another basic question: why you set p=u/(sigma^2) and r=(u^2)/(sigma^2-u) ? How to explain it with intuition and mathematics as well? Thank you very much.

3. I also ran DESeq2 for my expression data, but I compare DESeq result with DESeq2 one, the number of differential expression miRNA is way more far. DESeq screen about 40 out of 1040 miRNAs, while DESeq2 screen about 400more out of 1040 miRNAs. Furthermore, the rank of these screened miRNAs is also inconsistent. So could you give some rough ideas to explain the difference between the two tools? Thank you.
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