Moderator: Michael Love

gravatar for Michael Love
Michael Love16k
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16,020
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Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
1 day, 2 hours ago
Joined:
4 years, 11 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 • 3,182 results • page 2 of 319 • next >
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Answer: A: DESeq2 - MAP and MLE - log2FoldChange
... You're using a newer version of DESeq2. See the NEWS file for changes. In particular the relevant one was from a year ago, when DESeq() now outputs MLE fold changes. This is described in NEWS and in the vignette. ...
written 4 days ago by Michael Love16k
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Answer: A: To analyze the overall variance, which one to choose, vst or DESeq2 normalized c
... I recommend the vst(). It will help you compare variances across genes. You could also use rlog() I just prefer vst() these days. ...
written 5 days ago by Michael Love16k
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Comment: C: design versus interaction term similarities and/or differences?
... Sorry these questions don’t really make sense and I can’t answer them meaningfully.   ...
written 5 days ago by Michael Love16k
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Comment: C: DESeq2 interaction term
... yes ...
written 5 days ago by Michael Love16k
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Answer: A: DESeq2 package - different results
...  This is one of the frequently asked questions in the FAQ in the vignette; please take a look. ...
written 5 days ago by Michael Love16k
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Comment: C: design versus interaction term similarities and/or differences?
... That will give you something like an ANOVA. But it is also a test of differential expression. ...
written 5 days ago by Michael Love16k
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Comment: C: design versus interaction term similarities and/or differences?
... It sounds like you could accomplish all of this with pairwise comparisons using results() and contrast with the group variable as you have it above.  This will give you Wald test statistics and adjusted p values, which can be used by downstream software packages.  ...
written 5 days ago by Michael Love16k
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Answer: A: DESeq2-No replicates-Utility of log2fold shrunk values?
... For no replicate experiments, I'd suggest applying the vst() and then you can just calculate the simple difference between the two samples. This will give you a log2 fold change that is moderated, such that small counts do not produce large LFC (avoiding having to pick a pseudocount). ...
written 6 days ago by Michael Love16k
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Answer: A: design versus interaction term similarities and/or differences?
... "One of my main objectives is to identify drought-responsive genes." Can you be more specific than this? What hypotheses do you want to test? ...
written 6 days ago by Michael Love16k
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Answer: A: lfcShrink: Error when using numerical contrast vector
... hi Amal, Thanks for this report. It's tricky to use a numeric or list-style contrast here. Using 'contrast' with type="normal" makes use of expanded model matrices. And so the numeric or list need to reference coefficients from an expanded model matrix, but you don't see those when you run resultsN ...
written 7 days ago by Michael Love16k

Latest awards to Michael Love

Scholar 8 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 8 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 8 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Student 8 months ago, asked a question with at least 3 up-votes. For recount counts in the example experiment
Appreciated 8 months ago, created a post with more than 5 votes. For A: DESeq2 Model Design
Scholar 9 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Student 9 months ago, asked a question with at least 3 up-votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Commentator 9 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 9 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 Model Design
Scholar 9 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 9 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 9 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 9 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 9 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 9 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 9 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 9 months ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Appreciated 9 months ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 9 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 10 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 10 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 10 months ago, created a post with more than 5 votes. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 10 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 10 months ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Appreciated 11 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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