Moderator: Michael Love

gravatar for Michael Love
Michael Love16k
Reputation:
16,000
Status:
Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
14 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 1 of 319 • next >
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Comment: C: Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Tran
... I use Gencode, because I usually work with Ensembl txps downstream. Also they have made it easy to download the various files for different versions and organisms. I find it hard to navigate RefSeq. ...
written 14 hours ago by Michael Love16k
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Comment: C: Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Tran
... You can use the development branch (release in April) of tximport, and use the argument ignoreAfterBar. For Salmon, you would use the “gencode” flag to clean up the txp names.   ...
written 14 hours ago by Michael Love16k
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Answer: A: GC content and length bias in RNA-seq data
... The last line does nothing, and can be skipped. The rest is correct. (Except the runif(), presumably there just for demonstration.) BTW, to notify the developers of a post here, you can add the package name as a tag. This will trigger an email to the maintainer. ...
written 16 hours ago by Michael Love16k
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Comment: C: Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Tran
... I just changed the development branch to print out some of the IDs so users can more easily see the descrepancy. ...
written 21 hours ago by Michael Love16k
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Answer: A: Constructing tx2gene for Salmon txImport Quantification using Gencode Mouse Tran
... The best way to start diagnosing this is to look at the names of the transcripts in the quant.sf files. Can you show some of these? You should then compare to the transcript names in tx2gene. These need to be the same. If there is an extra version digit(s) in the quant files, you should use the igno ...
written 23 hours ago by Michael Love16k
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Answer: A: Re-calculate DESeq from dds based on another design
... You need to add a variable to the design, and then re-run DESeq(). This isn't done automatically by adding a factor to the data set for many reasons, mostly (1) because the design is what tells exactly how you intend to model the counts using the variables, and (2) because users often have more vari ...
written 23 hours ago by Michael Love16k
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Answer: A: find gene only express in one condition in Deseq2
... We don’t have a concept of what is expressed or not, that is we don’t distinguish betweeen small counts from lowly expressed vs “not expressed”. ...
written 1 day ago by Michael Love16k
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Comment: C: To analyze the overall variance, which one to choose, vst or DESeq2 normalized c
...  Please check out the vignette and workflow sections on transformations. We cover both of these questions there. ...
written 1 day ago by Michael Love16k
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Comment: C: DESeq2 interaction term
... You can use this genotype as well. This is an advantage of having all the samples in one model, as the information about variability among replicates is shared among genotypes. ...
written 1 day ago by Michael Love16k
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Comment: C: DESeq2 LFC shrinkage is for designs with interactions
... This is expected. apeglm will give back an LFC of near 0 if there is essentially no information to estimate the actual LFC. We'll have a manuscript up soon describing the methods. ...
written 1 day 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 8 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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