User: Daniel

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Daniel10
Reputation:
10
Status:
New User
Location:
Finland
Last seen:
5 months, 2 weeks ago
Joined:
5 years, 2 months ago
Email:
d**************@gmail.com

Posts by Daniel

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Design matrix for continuous independent variable in limma
... Hello Aaron, does this work also in the more "extreme" case when `age` is constant, like for example `age <- rep(1,35)` instead of `age <- runif(35, 20, 50)` Housekeeping/reference genes are expected to be more or less constantly expressed. ...
written 5 months ago by Daniel10
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Answer: A: justRMA and wrong customCDFs causing segfault
... It looks that even now this bug is not fixed yet. In my case justRMA still fails with segfault with custom CDF files (even that it works just fine with each individual CEL files). ...
written 7 months ago by Daniel10
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Comment: C: limma roast syntax and interpretation
... what exactly is e here (from "roast(e, myIndex, design, contrast=cont.matrix, nrot=5000)")? ...
written 7 months ago by Daniel10
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Comment: C: estimateDisp runs forever but not the trio estimateGLM
... > That's strange, estimateDisp should be faster than the trio. In my case is the other way around. estimateDisp runs ~30 minues while the trio estimateGLM run in less than 2 minutes. > it's odd that one would run forever and the others would be faster I agree. > Are you using the latest ...
written 3.5 years ago by Daniel10
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estimateDisp runs forever but not the trio estimateGLM
... Hello,   I get this "y = estimateDisp(y, design, robust = TRUE)" running forever even that the trio estimateGLM runs just fine (and I am able to finish the DE analysis with them and using glmFit and glmLRT). Therefore, is it safe to replace "y = estimateDisp(y, design, robust = TRUE)" with the tr ...
edger estimatedisp written 3.5 years ago by Daniel10 • updated 3.5 years ago by Aaron Lun24k
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Comment: C: edgeR: no replicates & mroast
... Sorry for not being very clear with my question. In my question above I was meaning by "forcing" that one could "borrow" the (i) dispersion _and_ (ii) residual degrees of freedom from somewhere else (e.g. from different time-point). Already in the example from above the dispersion is "borrowed" (i.e ...
written 4.7 years ago by Daniel10
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Comment: C: edgeR: no replicates & mroast
... Again this example is great! Thank you! Daniel ...
written 4.7 years ago by Daniel10
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edgeR: no replicates & mroast
... Hello, the edgeR manual (i.e. user guide that was last revised 25 September 2014) explains very nicely, with nice examples, what to do when there are no replicates. For example, for at section 2.10, sub-section 2 (that is picking a dispersion value, based on your experience with similar data, and ...
edger roast written 4.8 years ago by Daniel10 • updated 4.8 years ago by Gordon Smyth38k
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total count filter cutoff (edgeR)
... Gordon K Smyth writes: > > Hi Mahnaz, > > Why don't you follow the advice of the edgeR User's Guide (as Mark has > suggested)? All the case studies in the User's Guide describe how the > filtering was done in a principled way. > > Total count filtering is not so bad, but ...
mirna edger written 5.2 years ago by Daniel10

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Popular Question 3.5 years ago, created a question with more than 1,000 views. For edgeR: no replicates & mroast

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