Moderator: Michael Love

gravatar for Michael Love
Michael Love22k
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United States
Website:
http://mikelove.github...
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mikelove
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Joined:
6 years, 1 month 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 • 4,639 results • page 1 of 464 • next >
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Answer: A: Manually feed DESeq with dispersions
... You can just use dispersions(dds) <- ... to supply your own dispersion estimates rather than estimating them with DESeq2. Instead of running DESeq() you would run the individual steps, see ?DESeq. ...
written 1 hour ago by Michael Love22k
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Comment: C: DESeq2: How does the model of the trend function looks like?
... The subtraction is from what you would expect with a hierarchical Normal. The variances of the Normals add, so to get a reasonable prior from the observed distribution, we subtract the expected sampling variance. ...
written 1 hour ago by Michael Love22k
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Answer: A: DESeq2: How does the model of the trend function looks like?
... By the way, if you want to see how it looks, you can run `plotDispEsts`, which plots the dispersion estimates. https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#dispersion-plot-and-fitting-alternatives The trend function is: alpha_tr(x) = a1 / x + a0 No error, ...
written 1 day ago by Michael Love22k
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Answer: A: Three-factor design with DESeq2
... One recommendation I'd have for you is that many of your questions can be easily answered by running a model with a subset of the data. E.g to answer the first question, subset to species A and run a simple time series model with `~time + treatment + treatment:time`. This will answer your question d ...
written 1 day ago by Michael Love22k
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Comment: C: Installing DESeq2 on Google Cloud
... This issue with the devel libraries comes up so frequently, it's even a FAQ in the DESeq2 vignette :-) ...
written 1 day ago by Michael Love22k
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Answer: A: error in addIds
... We look up the correct organism in `tximeta` using the string that you specify, where `Homo Sapiens` gives `HS` as the string. This would work if you specify the organism in `makeLinkedTxome` as `Homo sapiens`. ...
written 2 days ago by Michael Love22k
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Answer: A: DESEQ2 normalization vs Subsampling
... I'm not sure I understand the question fully. Are you referring to the size factor estimation? The median ratio method is fairly robust to the kind of differences seen in typical RNA-seq experiments. If you are concerned about a particular experiment, and global changes to the distribution, you coul ...
written 2 days ago by Michael Love22k
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Comment: C: Analyzing nested experimental conditions in DESeq2
... I’d recommend working with a statistician if it’s your first time working with linear models. Or you can take at look at the workflow and vignette which are fairly extensive. I unfortunately don’t have too much time for statistical questions and have to reserve my time for software related questions ...
written 2 days ago by Michael Love22k
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Answer: A: Analyzing nested experimental conditions in DESeq2
... Yes, that's the design I would use depending on your experimental questions. Take a look at the DESeq2 workflow which has a time series example (only two conditions, but you can compare the code which is similar). ...
written 2 days ago by Michael Love22k
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Answer: A: RPM data analysis with DESeq2
... Not really. If you don't have access to the counts or quantification data, I would not recommend to use DESeq2. ...
written 2 days ago by Michael Love22k

Latest awards to Michael Love

Teacher 3 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 3 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Teacher 3 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 3 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Appreciated 3 months ago, created a post with more than 5 votes. For A: DESeq2 baseMean values for each sample
Scholar 3 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 4 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 4 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 4 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 4 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 4 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 5 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 5 months ago, created an answer that has been accepted. For A: DESeq2 - Three Sample Analysis
Scholar 5 months ago, created an answer that has been accepted. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Scholar 5 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Teacher 5 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 5 months ago, created an answer that has been accepted. For A: Should I use alpine and can I convert the output back to counts?
Appreciated 5 months ago, created a post with more than 5 votes. For A: How does DESeq2 handle zero counts in one condition?
Great Question 5 months ago, created a question with more than 5,000 views. For New function lfcShrink() in DESeq2
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 1.20.0 lfcshrink function
Scholar 5 months ago, created an answer that has been accepted. For A: DESeq2 on two groups
Prophet 5 months ago, created a post with more than 20 followers. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: DESeq2 why estimate dispersion on log scale

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