Moderator: Michael Love

gravatar for Michael Love
Michael Love24k
Reputation:
23,840
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
3 days ago
Joined:
6 years, 4 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 • 4,888 results • page 2 of 489 • next >
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Comment: C: EdgeR - Model matrix for complex model similar to user guide 3.5 example - but m
... I’ve changed the tags. Please don’t add additional packages to the question because it emails all the developers when you tag a post. If you have an edgeR question it’s appropriate to tag with “edgeR”. ...
written 6 days ago by Michael Love24k
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Comment: C: exomeCopy compileCopyCountSegments error
... It looks like the reason it returns NULL is because there are many 0’s. ...
written 7 days ago by Michael Love24k
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Comment: C: exomeCopy compileCopyCountSegments error
... It looks like the reason it returns NULL is because there are many 0’s. ...
written 7 days ago by Michael Love24k
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Answer: A: Creating the correct design
... Take a look at the vignette section on interactions first. Secondly, if you want to do some exploration, use `plotCounts` on the top genes to understand why they are identified as DE. ...
written 8 days ago by Michael Love24k
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Answer: A: Using altHypothesis with shrunken LFC values in DESeq2
... You don't want to use shrunken LFC for when your alternative hypothesis is that the genes are less than theta in absolute value (and the software won't allow this), see the DESeq2 paper for discussion. ...
written 8 days ago by Michael Love24k
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Answer: A: Paired samples in cell lines using DESeq2
... Yes, that is the correct model, `~patient + condition` (it's good to put condition last in general, see vignette for details). ...
written 8 days ago by Michael Love24k
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Comment: C: deseq2 pre filter rna seq
... Correct. We do sometime perform minimal pre-filtering. Mostly this is to reduce unnecessary computation, whereas the independent filtering (or better yet, IHW) is for increasing power. There is no need to run DESeq2 for bulk RNA-seq on genes where only one or two samples have a single digit count an ...
written 8 days ago by Michael Love24k
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Answer: A: Analysis strategy - possible to use naive control group as t=0 for two treatment
... I'd echo James' point that you may do well to discuss the statistical approach with a local collaborator. For DESeq2 you're probably just best off having a factor `group` with levels for all the 5 groups. You can then do pairwise comparisons. Unlike the time course example in the vignette, you can' ...
written 8 days ago by Michael Love24k
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Answer: A: exomeCopy compileCopyCountSegments error
... I haven't touched exomeCopy in years, maybe since 2011, so I don't remember the details. Perhaps there are no calls in `fit.list`? Can you plot one of the fits to see if there are any calls outside of copy number = 2? ...
written 8 days ago by Michael Love24k
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Comment: C: DESeq2: Second order interactions
... I'd highly recommend discussing with a statistician. With a complex design like this, with repeated measures and three interacting covariates, I would typically meet with a local investigator to discuss analysis plans and assumptions face-to-face, including the entire team. It's not just getting the ...
written 9 days ago by Michael Love24k

Latest awards to Michael Love

Scholar 6 months ago, created an answer that has been accepted. For A: clarification of time-series analysis
Scholar 6 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Scholar 6 months ago, created an answer that has been accepted. For A: DESeq2 - Three Sample Analysis
Scholar 6 months ago, created an answer that has been accepted. For A: What is the biological meaning of genes with FC = 0 after shrinkage
Scholar 6 months ago, created an answer that has been accepted. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Deseq2: RNA-seq and Negative binomial distribution
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: clarification of time-series analysis
Scholar 6 months ago, created an answer that has been accepted. For A: Should I use alpine and can I convert the output back to counts?
Scholar 6 months ago, created an answer that has been accepted. For A: DESeq2 on two groups
Scholar 6 months ago, created an answer that has been accepted. For A: Change lower bound 'optim' function in DESeq2::unmix() to 0.001 to prevent error
Scholar 6 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 6 months ago, created an answer that has been accepted. For A: Unable to find an inherited method for function 'results' for signature '"DESeqD
Scholar 6 months ago, created an answer that has been accepted. For A: Using altHypothesis with shrunken LFC values in DESeq2
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: How does DESeq2 handle zero counts in one condition?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Common differentially expressed genes between two cell lines
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: [DESeq2] time series strain-specific differences over time
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: DESeq2 baseMean values for each sample
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?
Scholar 6 months ago, created an answer that has been accepted. For A: Using alternative LFC shrinkage methods for computing p-values in DESeq2
Scholar 6 months ago, created an answer that has been accepted. For A: DESeq2::sizeFactors() function does not output the sizeFactor table.
Scholar 6 months ago, created an answer that has been accepted. For A: How to extract factor levels of coldata from deseq object?
Scholar 6 months ago, created an answer that has been accepted. For A: DESeq2 lfcShrink using only dds and res arguments
Scholar 6 months ago, created an answer that has been accepted. For A: Multiple groups and two methods to analyse them with DESeq2
Scholar 6 months ago, created an answer that has been accepted. For A: How to find Top 10 expressed genes in DESeq2

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