User: jake.hagen

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jake.hagen50
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New User
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United States
Last seen:
3 years, 2 months ago
Joined:
5 years ago
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j*********@opmbx.org

Posts by jake.hagen

<prev • 6 results • page 1 of 1 • next >
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Comment: C: Trimmomatic -> STAR
... I don't trim reads when using star, as I believe it includes soft trimming when aligning reads. Is there a special reason you are using hard trimming? or and argument for using trimmomatic? Thanks ...
written 3.3 years ago by jake.hagen50
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Comment: C: Is inspection and correction of pvalues still needed in DESeq2?
... It has been a while since I looked at this, I am not sure what I ended up doing (probably just followed the manual without empirically estimating the null model variance). Do you have more than two conditions in which you model together? This was my case for the above plot, and if I was facing the ...
written 3.4 years ago by jake.hagen50
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Comment: C: A strange R limma voom function mean-variance trend
... For future reference I wasn't able to view your image, it wanted me to sign in. Maybe it needs to be shared differently, or maybe it is just me.  ...
written 5.0 years ago by jake.hagen50
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Answer: A: install qvalue in R
... You need to install a package for your linux distribution. Look at this discussion http://r.789695.n4.nabble.com/Where-is-the-tcltk-package-td3434915.html For example, from the link above > (3) Under Ubuntu Linux you can obtain the aforesaid development version by: > >    sudo apt-get in ...
written 5.0 years ago by jake.hagen50
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Comment: C: Is inspection and correction of pvalues still needed in DESeq2?
... Thank you for the reply. I understand now that plotting the pvalue distribution is a diagnostic step and is not specific to the DESeq2 package.  I am struggling with when and why to adjust pvalues with empirical null modeling. The way I read the linked tutorial it would seem it should be done whenev ...
written 5.0 years ago by jake.hagen50
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Is inspection and correction of pvalues still needed in DESeq2?
... While trying to better understand the inner-workings of the DESeq2 package I came across this tutorial: http://www-huber.embl.de/users/klaus/Teaching/DESeq2-Analysis.pdf The part that confused me was 5.2.2, the inspection and correction of p-values, I had not seen anything like that in the DESeq2 ...
deseq2 rna-seq written 5.0 years ago by jake.hagen50 • updated 3.4 years ago by EVR570

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