Moderator: Michael Love

gravatar for Michael Love
Michael Love15k
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Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Last seen:
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Joined:
4 years, 8 months ago
Email:
m****************@gmail.com

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

My main Bioconductor involvement is to maintain these software packages

and the RNA-seq gene-level workflow.

Posts by Michael Love

<prev • 2,869 results • page 2 of 287 • next >
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Answer: A: Multi Anova in DESeq2
... hi, Sorry I missed this post because it didn't have a "deseq2" tag (it had "anova deseq2", but the support site only uses exact tags to notify maintainers). If it's not too late, the recommended design would be the above and then use a LRT with a reduced design of ~mutA + mutB. dds <- DESeq(d ...
written 3 days ago by Michael Love15k
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Answer: A: How can I use DESeq2 for exploratory analysis after batch effect removal using R
... You can use limma's removeBatchEffect(x, batch) with the transformed data matrix (assay(vsd) or assay(rld)) and the W column from RUV. This will remove mean shifts in the transformed counts associated with the W column. This is similar to what is done inside of the model when you run DESeq() with a ...
written 4 days ago by Michael Love15k
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Comment: C: Multiple differential expression analyses with DESeq2
... No you can't change the design after calculating dispersion. The dispersion only make sense relative to a certain design. Imagine, if you set ~1, and you have a gene with DE across two groups of samples. You will get a high dispersion estimate, because the design doesn't allow for different mean co ...
written 4 days ago by Michael Love15k
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Comment: C: SNP-level Allele-specific expression detection using DESeq2 in an unpaired exper
... hi Stephan, I'm not sure about the point of glm.nb. You can use estimateDispersionsGeneEst() to quickly obtain the MLE dispersions. These are stored in mcols(dds)$dispGeneEst, and you can set them to be final with dispersions(dds) <- x. n=10 per group is ok, depending on how many groups, you may ...
written 4 days ago by Michael Love15k
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Answer: A: DESeq2 for differential gene expression on GTEx dataset
... hi, For 100s of samples per condition/group, and with a total of thousands of samples overall, for differential expression I personally tend to switch to faster linear models, like limma-voom. The GLM has to do a lot of computation to iteratively find the solution (a beta coefficient for each tissu ...
written 4 days ago by Michael Love15k
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Answer: A: Multiple differential expression analyses with DESeq2
... 1) yes 2) do you mean comparing groups? Take a look at the ‘contrast’ argument in this help file: ?results 3) if you have prespecifed the genes before you look at the data, then yes you could recompute BH adjustment just on your genes of interest, but peeking at the data first and then choosing t ...
written 5 days ago by Michael Love15k
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Comment: C: Filtering DESeq2 result export along multiple lines
... Usually we do treated / vehicle, which you can obtain by setting the reference level of the condition variable before you run DESeq(), see this section: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#note-on-factor-levels You can get beta > 2, beta < -2 ...
written 7 days ago by Michael Love15k
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Comment: C: Filtering DESeq2 result export along multiple lines
... Let's go from the other direction: what kind of LFC are you interested in finding when you compare treatment to vehicle? ...
written 7 days ago by Michael Love15k
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Comment: C: Filtering DESeq2 result export along multiple lines
... Are you interested in finding genes with large LFC (in absolute value)? If so, you should use the default value for altHypothesis. See the DESeq2 paper or vignette for more details. ...
written 7 days ago by Michael Love15k
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Comment: C: tximport returns NA counts
... Thank Leon for the useful feedback here. We can either have a specific read_tsv importer for each method 'type' that explicitly sets the col_types, or I could set guess_max=Inf so that read_tsv uses the full file for setting col_types. The first approach should be faster, so I'll probably go with t ...
written 7 days ago by Michael Love15k

Latest awards to Michael Love

Scholar 5 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 5 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 5 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Student 5 months ago, asked a question with at least 3 up-votes. For recount counts in the example experiment
Appreciated 5 months ago, created a post with more than 5 votes. For A: DESeq2 Model Design
Scholar 5 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Student 5 months ago, asked a question with at least 3 up-votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 Model Design
Scholar 6 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Scholar 6 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Popular Question 6 months ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Popular Question 6 months ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Appreciated 6 months ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 6 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 7 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Is the VST implemented in DESeq useful on time-series cell differentiation datas
Appreciated 7 months ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 7 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 7 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Appreciated 8 months ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)

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