Moderator: Michael Love

gravatar for Michael Love
Michael Love18k
Reputation:
17,790
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
2 hours ago
Joined:
5 years, 3 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:

and the RNA-seq gene-level workflow.

Posts by Michael Love

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Comment: C: DESseq2: Why can the dispersion be generelized over the conditions?
... DESeq2 is a pretty standard GLM but with a hierarchical model for dispersion. It might help to read some background on GLM first (lots of free courses online). The question you have is more about how GLMs work than DESeq2 in particular. ...
written 2 hours ago by Michael Love18k
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Comment: C: The calculation of regularized logarithm
... Not exactly, but it’s a somewhat related point. That post is about estimated LFCs and your question is about the rlog. ...
written 6 hours ago by Michael Love18k
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Comment: C: Visualization for Time Course "LRT" test in DESeq2
... Oh I see, you want to see all genes at once. We don’t have a visualization scheme for this. ...
written 7 hours ago by Michael Love18k
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Answer: A: Visualization for Time Course "LRT" test in DESeq2
... Have you seen the plot that we make in the workflow section on time course? https://bioconductor.org/packages/3.7/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#time-course-experiments ...
written 7 hours ago by Michael Love18k
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Comment: C: DESeq2 - how to build design for matched case-control study with repeated measur
... You would use the strategy in the vignette for testing for condition effects within and across groups while controlling for individuals nested within groups. ...
written 1 day ago by Michael Love18k
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Comment: C: The calculation of regularized logarithm
... Yes, that is the log q_ij we are after, except the standard X is not used but a different one (see the paper Methods and vignette -- the link I gave above -- for full details). We write log in the Methods, but convert to log2 whenever we give output to the user. So you can imagine it is log2 q_ij. ...
written 1 day ago by Michael Love18k
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Answer: A: The calculation of regularized logarithm
... Yes, rlog is log2(q_ij). I think this formula is clear: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#regularized-log-transformation The formula you find in the above link is the same as in the Regularized logarithm section in the Methods of the DESeq2 paper. ...
written 2 days ago by Michael Love18k
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Answer: A: DESeq2 - how to build design for matched case-control study with repeated measur
... With fixed effects, we can't include the matching variable and also a variable to distinguish the two individuals within the control, because these are confounded variables. In general, you can instead use limma with the duplicateCorrelation() correlation function when fixed effects cannot be used b ...
written 2 days ago by Michael Love18k
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Comment: C: Deseq2 problem visualizing gene expression with batch corrected values
... Can you post the plotCounts() for this gene straight from DESeq2? This may help us see the differences better. Also, what is the mean of VST values in the two groups (after you've used removeBatchEffect)? ...
written 2 days ago by Michael Love18k
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Comment: C: 2x2 design - UP means more expression on S than R and DOWN less expression on S
... Please post your code, including the design, and the colData so we can have a better idea of what you are doing. http://www.bioconductor.org/help/support/posting-guide/ ...
written 2 days ago by Michael Love18k

Latest awards to Michael Love

Scholar 5 weeks ago, created an answer that has been accepted. For A: DESeq2 why estimate dispersion on log scale
Scholar 5 weeks ago, created an answer that has been accepted. For A: DESeq2 confounding cartridge
Scholar 5 weeks ago, created an answer that has been accepted. For A: Post-processing RNA-Seq after tximport
Scholar 5 weeks ago, created an answer that has been accepted. For A: Unexpected differences in results from paired analysis with DESeq2
Scholar 5 weeks ago, created an answer that has been accepted. For A: Analysis guidance for data inclusion in deseq2 analysis: data subsets vs contras
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: DESeq2 biais when genes are missing from the annotation?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to get DESeq2 sizefactors from data imported using tximport
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Analyzing RNA-Seq data without replicates using DESeq
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: What to use: PCA or tSNE dimension reduction in DESeq2 analysis?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: identifying the samples on plotPCA
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Student 12 months ago, asked a question with at least 3 up-votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: DESeq2 batch effect with and without interaction model
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: DESeq2 paired multifactor test
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How does DESeq2 handle zero counts in one condition?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: DESeq2: add annotations (from data frame) to DESeqDataSet
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: GC/length bias correction in gene expression quantification - Is CQN necessary i
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: tximport with versioned identifiers
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Normalize to additional variable (brain weight) in DESeq2
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: deseq2 - many differentially expressed genes
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: deseq2 estimating size factors
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: DESeq2 Model Design
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: DESeq is better than DESeq2?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: DESeq2 batch effect modeling and matrix not full rank

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