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Old 12-22-2011, 05:14 AM   #21
anle
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Quote:
Originally Posted by Simon Anders View Post
There is no letter 'O'. This is a zero. I wanted to write 'q0' with zero as subscript but did not manage. (Don't know if the forum software allows subscripts.) So, 'q0' is one value (and distinct from q, which I use further down for the realization of the random variable Q) and 'a' is the other one.

I specified the first two moments. Solving the expressions for them for the shape and scale parameter, you get for the scale a q0 and for the shape 1/a.

By the way, this is all frequentist statistics. There is nothing Bayesian in here.
Thnx!! Sorry I was misconfused but marginalization and conditional probabilities make me think of Bayes
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Old 08-12-2014, 02:38 PM   #22
chaoxing
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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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Old 08-12-2014, 02:56 PM   #23
Simon Anders
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Please don't highjack an old thread to post unrelated questions. This makes it impossible for other readers to find pertinent information.

Also, please don't put several unrealted questions into the same thread.

Finally, I have sent you the link to this thread when you asked the same question by e-mail, because I feel that it answers your first question. Have you read the thread? Did it answer your question? If not, what is unclear about the equations?
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Old 08-12-2014, 02:57 PM   #24
Simon Anders
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Finally, I have no clue what you mean with p and r. I don't recall using these letters in our paper.
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Old 08-12-2014, 03:42 PM   #25
chaoxing
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Pr(K=k)=(k+r-1,r-1)p^r(1-p)^k,
you set p=u/sigma^2, r=u^2/(sigma^2-u),

p and r are derived from here.

Thank you.
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