User: Nik Tuzov

gravatar for Nik Tuzov
Nik Tuzov70
Reputation:
70
Status:
Trusted
Location:
United States
Website:
https://www.linkedin.c...
Last seen:
5 months ago
Joined:
4 years, 2 months ago
Email:
n*****@partek.com

Posts by Nik Tuzov

<prev • 57 results • page 1 of 6 • next >
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Comment: C: FCSTransTransform() implementation in flowCore
... Thanks for replying. Do you think the automatic width calculation inside FCSTransTransform() is helpful and often used? ...
written 5 months ago by Nik Tuzov70
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FCSTransTransform() implementation in flowCore
... Hello: It looks like the only difference (please correct me if I'm wrong) from FCSTrans implementation is that flowCore uses it's own C++ implementation of biexponential_transform() in place of original C implementation in FCSTrans. 1) If FCSTransTransform() was meant to reproduce FCSTrans, why wa ...
flowcore flow cytometry fcstrans written 5 months ago by Nik Tuzov70 • updated 5 months ago by Jake Wagner130
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Comment: C: Estimation of non-trivial contrasts in MAST
... There is a definite difference between MAST in DESeq2 when designs with interactions are considered. In MAST, all of the regression coefficients are shrunken in the logistic part no matter what, whereas in DESeq2 the shrinkage of regression coefficients is disabled when interactions are present: ht ...
written 6 months ago by Nik Tuzov70
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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 8 months 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 8 months 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 8 months 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 8 months ago by Nik Tuzov70 • updated 8 months 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 8 months 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 8 months ago by Nik Tuzov70 • updated 8 months 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 2.1 years ago by Nik Tuzov70

Latest awards to Nik Tuzov

Popular Question 5 months ago, created a question with more than 1,000 views. For Limma-voom vs limma-trend
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Limma-voom vs limma-trend
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Normalization methodology in DESeq/DESeq2 vs edgeR
Popular Question 2.1 years ago, created a question with more than 1,000 views. For What was the very first paper to describe "limma-trend"?
Supporter 2.9 years ago, voted at least 25 times.
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Normalization methodology in DESeq/DESeq2 vs edgeR

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