User: Nik Tuzov

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Nik Tuzov70
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70
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Trusted
Location:
United States
Website:
https://www.linkedin.c...
Last seen:
1 day, 14 hours ago
Joined:
3 years, 6 months ago
Email:
n*****@partek.com

Posts by Nik Tuzov

<prev • 54 results • page 1 of 6 • next >
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Comment: C: Estimation of non-trivial contrasts in MAST
... Hello Andrew: What happens in contrast estimation if there is a quantitative covariate? E.g. I have the following toy data set: y <- c(0.0, 0.0, 0.01981825833, 0.40109357786, 0.34727231426, 0.03889038132, 0.0, 0.0, 0.11225699507, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.90902480961) ...
written 3 days ago by Nik Tuzov70
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Comment: C: Estimation of non-trivial contrasts in MAST
... Hello Andrew: You are probably familiar with [this paper of Soneson and Robinson][1]. Their overall conclusion is that the best single-cell-specific method was MAST, but it did as well as the best of bulk RNA methods. Do you think they got something wrong? [1]: https://www.nature.com/articles/nm ...
written 6 days ago by Nik Tuzov70
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Comment: C: Logistic regression in MAST - question
... Hello Andrew: Thanks for replying. If I don't want to create SingleCellAssay object, how can I put a number of transcripts in a data frame to do a similar analysis. Do I need to somehow add TranscriptID column to that simulated data frame? ...
written 9 days ago by Nik Tuzov70
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Logistic regression in MAST - question
... Hello: I am trying to reproduce an example given in MAST reference for zlm() where a data frame with 500 points is used. I assume this data set describes one single feature, hence no shrinkage is applied. I managed to reproduce the continuous part. The regression coefficients for the discrete pa ...
mast written 10 days ago by Nik Tuzov70 • updated 10 days ago by Andrew_McDavid190
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Comment: C: Estimation of non-trivial contrasts in MAST
... Hello Andrew: Thanks for replying. I also have a MAST specific question. The paper describes how shrinkage is done but it says little about why it was necessary in the first place. What kind of evidence did you get to justify the application of shrinkage? Regards, Nik ...
written 10 days ago by Nik Tuzov70
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Estimation of non-trivial contrasts in MAST
... Hello: Could you tell me if there is an easy way to estimate non-trivial contrasts in MAST? E.g. there are two factors, A and B, with 3 and 5 levels, the model is Y = A + B + A*B, and I want to test (A1, B2) vs (A2, B5). I assume the answer is no because a similar [question][1] was asked of DESeq2 ...
mast written 13 days ago by Nik Tuzov70 • updated 10 days ago by Andrew_McDavid190
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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 17 months ago by Nik Tuzov70
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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 18 months ago by Nik Tuzov70
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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 18 months ago by Nik Tuzov70
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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 18 months ago by Nik Tuzov70

Latest awards to Nik Tuzov

Supporter 2.2 years ago, voted at least 25 times.
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Normalization methodology in DESeq/DESeq2 vs edgeR

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