Moderator: Michael Love

gravatar for Michael Love
Michael Love15k
Reputation:
14,560
Status:
Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
21 hours ago
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 1 of 287 • next >
0
votes
1
answers
87
views
1
answers
Comment: C: deseq2 analysis with multiple factors and interaction terms
... hi, If you code treatment so that it has three levels, "control","time30m", and "time60m", you can use a design, ~genotype + time + genotype:treatment. This will provide four interaction terms for genotype x the two treatment effects, and you can contrast these using the 'list' style of contrast i ...
written 21 hours ago by Michael Love15k
0
votes
1
answers
87
views
1
answers
Answer: A: deseq2 analysis with multiple factors and interaction terms
... Re: "whether the treatment effect is different over genotype" I like to start things off by asking how you want time to be included. One possibility is to consider a 30 min treatment effect and a 1 hour treatment effect and look at how these two effects are different over genotype. I'm assuming you ...
written 1 day ago by Michael Love15k
0
votes
2
answers
87
views
2
answers
Answer: A: Using tximport to convert a dataframe consisting of tpm to counts for use with l
... tximport requires the original files, as it uses more information than the TPM alone. See the tximport citation for more details. ...
written 1 day ago by Michael Love15k
0
votes
1
answers
67
views
1
answers
Answer: A: Running DESeq2 on top variable genes?
... This will cause problems with DESeq2's dispersion prior, which should see counts from all the genes, or at least not subsetted by having a high or low sample variance (across all samples). Without getting into the details, it's not a problem when you subset by sample mean, but it would be a problem ...
written 1 day ago by Michael Love15k
0
votes
1
answers
91
views
1
answers
Comment: C: Model matrix not full rank for condition-time experiment
... Starting a new comment thread for visual simplicity... You can use a design ~time + condition:time, but you need to recode "control" as "sham". Then there is an issue with using the design as formula (so when you specify the design just use ~time or anything here). You have to remove a column from ...
written 1 day ago by Michael Love15k
0
votes
1
answers
64
views
1
answers
Answer: A: DESeq2 Different Results when using different foreach parallel backends
... Can you confirm that the versions of DESeq2 are the same across all workers? It looks like some are using version < 1.16 where the default value was betaPrior=TRUE, where it is now FALSE. ...
written 1 day ago by Michael Love15k
0
votes
1
answers
91
views
1
answers
Comment: C: Model matrix not full rank for condition-time experiment
... I'm not following exactly the point about samples 1-8. Does Sham45.1 have a special relationship to Sham24.1, etc.? ...
written 2 days ago by Michael Love15k
0
votes
1
answers
91
views
1
answers
Comment: C: Model matrix not full rank for condition-time experiment
... "I want to find out the genes varying by condition over time." Do you want to find genes that vary by condition over time, meaning, comparing the non ischemic to the sham samples? So genes where the profile over time differs? Is there a relationship of the 1-8 samples at the two time points? Is sa ...
written 2 days ago by Michael Love15k
0
votes
1
answers
52
views
1
answers
Answer: A: DESeq2, lfcShrink, "Error in results(dds.shr, name = coefAlpha) : object 'co
... Thanks for reporting this bug. What version of DESeq2 are you using?  packageVersion("DESeq2") I can't reproduce this error with my version (1.18.1). Once I can reproduce it, I can try to find a solution. dds <- makeExampleDESeqDataSet() dds <- DESeq(dds) res <- results(dds) lfc <- ...
written 2 days ago by Michael Love15k
0
votes
1
answers
91
views
1
answers
Answer: A: Model matrix not full rank for condition-time experiment
... The vignette discusses the source of the problem in a special section (the error should have pointed you to this section): https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#model-matrix-not-full-rank Let's start from the beginning, what genes are you interested i ...
written 2 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)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 232 users visited in the last hour