User: Nik Tuzov

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Nik Tuzov60
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60
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Location:
United States
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https://www.linkedin.c...
Last seen:
1 month, 2 weeks ago
Joined:
2 years, 2 months ago
Email:
n*****@partek.com

Posts by Nik Tuzov

<prev • 48 results • page 1 of 5 • next >
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... Is this issue present even when the design is orthogonal? ...
written 7 weeks ago by Nik Tuzov60
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... The reason I asked the question was personal curiosity. Recently I started to review the older shrinkage methods (ridge, lasso, etc) that focus on shrinking the regression coefficients that describe the mean of response. At the time I had an impression that what popular DE packages did it "backwards ...
written 7 weeks ago by Nik Tuzov60
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... I think in practice it's hard to separate these two. As far as I know, the user will need a list of genes with LFC estimates that are practically different from 0, and they have to be statistically significant (low p-value or high posterior odds ratio). ...
written 7 weeks ago by Nik Tuzov60
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... Hello Michael: Given what Ryan said below, does lfcShrink follow the suggestion I posted here: https://support.bioconductor.org/p/71975/#72049 ...
written 7 weeks ago by Nik Tuzov60
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... "In particular, I believed it was undesirable to overdo the shrinkage because that would give a misleading impression to biologists." What exactly do you mean by "misleading impression"?  ...
written 7 weeks ago by Nik Tuzov60
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Comment: C: Why limma, edgeR, and DESeq did not implement fold change moderation first?
... Thank you for replying. I'm sorry I got your name wrong. I understood that the moderated t-stat resulted in the same ranking of genes as the posterior odds, but it's not clear why "The posterior odds of DE implies moderation of the variances but not of the means. " I am looking at this version of y ...
written 7 weeks ago by Nik Tuzov60
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Why limma, edgeR, and DESeq did not implement fold change moderation first?
... Hello: I have a rather general question about how and why Bayesian inference have been applied in limma, edgeR, and DESeq1-2.   In the simplest differential expression study there are two regression coefficients, an intercept and slope, the latter also denoted by log fold change. LFC estimates ob ...
limma edger deseq deseq2 written 7 weeks ago by Nik Tuzov60 • updated 7 weeks ago by Gordon Smyth32k
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Comment: C: Seeking confirmation on manually setting contrasts for a 3-factor design in DESe
... If the user can only feed full rank designs to DESeq2, do you know if there is an R package that could help figure out how to specify contrast coefficients for non-trivial cases? If not, it's very hard to use the design produced by model.matrix() if the goal is to estimate non-trivial contrasts. ...
written 12 weeks ago by Nik Tuzov60
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Comment: C: modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
... Could you link the paper please? ...
written 12 weeks ago by Nik Tuzov60
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Comment: C: modeling zero-dominated RNA-seq with voom/limma and hurdle models (pscl)
... Have any of you looked at the prior weights when limma is applied to single cell data? In other words, how different are the results if you just run a Lognormal gene-specific model w/o shrinkage? Single cell has a larger sample size than bulk RNA, so I wonder if shrinkage becomes less necessary or m ...
written 12 weeks ago by Nik Tuzov60

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Popular Question 19 months ago, created a question with more than 1,000 views. For Normalization methodology in DESeq/DESeq2 vs edgeR

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