Moderator: Michael Love

gravatar for Michael Love
Michael Love19k
Reputation:
19,440
Status:
Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
13 hours ago
Joined:
5 years, 7 months ago
Email:
m****************@gmail.com

Michael I. Love, Dr. rer. nat.
Assistant Professor
Department of Biostatistics
Department of Genetics
University of North Carolina-Chapel Hill

The Love lab maintains the following R/Bioconductor packages:

the RNA-seq gene-level workflow, and the RNA-seq DTU workflow.

Posts by Michael Love

<prev • 3,973 results • page 1 of 398 • next >
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Comment: C: SVAseq and DESeq2 workflow
... I think it is too high, but I’ll leave it to the SVA developers to comment. ...
written 13 hours ago by Michael Love19k
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Comment: C: Dispersion fit and p-value distributions
... Going back, it seems like local dispersion fit fixes the p-value distribution. Bernd caught this although I missed the point on my first pass. ...
written 17 hours ago by Michael Love19k
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Comment: C: DESeq2 Time Series and "control" condition
... This was already answered in the thread here and it is discussed in the vignette. ...
written 23 hours ago by Michael Love19k
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Comment: C: DESeq2 Time Series and "control" condition
... You can perform the analysis across pairs of levels using the code that Simon posted. You just specify the two groups you want to compare with 'contrast' in the results() function. If DESeq() was run with test="LRT", then when you run results() you should also add test="Wald" to generate new p-value ...
written 1 day ago by Michael Love19k
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Answer: A: SVAseq and DESeq2 workflow
... You can use the example code in the workflow with any number of surrogate variables (or FUVs etc). The number of SVs seems too high here. 9 SVs for 11 samples? ...
written 1 day ago by Michael Love19k
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Comment: C: DESeq2 for large de novo transcripts assembly
... I see. Then maybe apeglm is preferred. If you use lfcThreshold with apeglm you will produce svalues that are consistent with the point estimates. ...
written 1 day ago by Michael Love19k
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Comment: C: DESeq2 Time Series and "control" condition
... So is everything clear or is there a remaining question? ...
written 1 day ago by Michael Love19k
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Comment: C: DESeq2 Time Series and "control" condition
... I’m not sure there’s a question left here that’s not answered in the vignette. The base level that you see in resultsNames is set alphabetically unless you do otherwise (see vignette “Note on factor levels”). The fact that a single coefficient appears at the top of the results table is explained at ...
written 1 day ago by Michael Love19k
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Comment: C: DESeq2 Time Series and "control" condition
... https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#i-ran-a-likelihood-ratio-test-but-results-only-gives-me-one-comparison. ...
written 1 day ago by Michael Love19k
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Comment: C: How to set up appropriate analysis using sample type and condition for DESeq2
... Yes. We carried over the option to do no replicate analysis from DESeq but the results weren’t even really meaningful, and I didn’t think it was appropriate to offer the option anymore, so we deprecated over a release cycle and then removed the option. For no replicates you can compute the vst() and ...
written 1 day ago by Michael Love19k

Latest awards to Michael Love

Scholar 6 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 6 weeks ago, created an answer that has been accepted. For A: DESeq2 on two groups
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: How does DESeq2 handle zero counts in one condition?
Scholar 6 weeks ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 6 weeks ago, created an answer that has been accepted. For A: DESeq2 - Three Sample Analysis
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2 baseMean values for each sample
Appreciated 10 weeks ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 10 weeks ago, created an answer that has been accepted. For A: DESeq2 - Three Sample Analysis
Appreciated 10 weeks ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 10 weeks ago, created an answer that has been accepted. For A: DESeq2 on two groups
Popular Question 10 weeks ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 10 weeks ago, created an answer that has been accepted. For A: Analysis guidance for data inclusion in deseq2 analysis: data subsets vs contras
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2 why estimate dispersion on log scale
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: What doest this p.value distribution mean?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How does DESeq2 handle zero counts in one condition?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2 baseMean values for each sample
Scholar 10 weeks ago, created an answer that has been accepted. For A: Post-processing RNA-Seq after tximport
Scholar 10 weeks ago, created an answer that has been accepted. For A: Should I use alpine and can I convert the output back to counts?
Scholar 4 months ago, created an answer that has been accepted. For A: Post-processing RNA-Seq after tximport
Scholar 4 months ago, created an answer that has been accepted. For A: DESeq2 confounding cartridge
Scholar 4 months ago, created an answer that has been accepted. For A: Analysis guidance for data inclusion in deseq2 analysis: data subsets vs contras
Scholar 4 months ago, created an answer that has been accepted. For A: DESeq2 why estimate dispersion on log scale
Scholar 4 months ago, created an answer that has been accepted. For A: Age covariate continuous vs. categorical
Scholar 4 months ago, created an answer that has been accepted. For A: Unexpected differences in results from paired analysis with DESeq2

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