Moderator: Michael Love

gravatar for Michael Love
Michael Love21k
Reputation:
20,810
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
4 hours ago
Joined:
5 years, 10 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 • 4,268 results • page 2 of 427 • next >
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Comment: C: Can I use DESeq2 for special assays
... I use housekeeping in my case and made MA plots to assess if the normalization was appropriate. It’s not easy to describe in general the various ways to assess the normalization but is somewhat specific to the experiment and the known biology and known technical factors. ...
written 3 days ago by Michael Love21k
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Answer: A: Can I use DESeq2 for special assays
... I’ve used DESeq2 with Nanostring data of 150 and 400 genes panels for example. The model works fine, but the critical piece is the library size correction. We used housekeeping probes to correct for library size. ...
written 3 days ago by Michael Love21k
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Answer: A: DeSeq2 Design for multiple cell lines, medias, vectors
... I’d recommend collaborating with a statistician to explore what type of statistical design to use to answer various questions. I don’t have time to provide extensive statistical consultation on this site but instead try to limit to software questions. ...
written 3 days ago by Michael Love21k
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Answer: A: Deseq2 Multiple condition issue
... When you type `resultsNames(dds)`, do you see `g1`? You should put the exact character string that you see in `resultsNames(dds)`, as the error message is indicating. ...
written 3 days ago by Michael Love21k
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Comment: C: Using varianceStabilizingTransformation (VST) with no replications?
... Any of those are valid choices. ...
written 4 days ago by Michael Love21k
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Comment: C: Using varianceStabilizingTransformation (VST) with no replications?
... Any of those are valid ...
written 4 days ago by Michael Love21k
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Comment: C: Using varianceStabilizingTransformation (VST) with no replications?
... You can run the VST on 6 samples without replication using `blind=TRUE` (the default) and `design=~1`. There's not a good case for end-users to use the `ignoreRank` argument. This is just for the DEXSeq package, kind of a backdoor. ...
written 4 days ago by Michael Love21k
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Comment: C: Getting wrong result using DESeq2
... Many genes are correlated, for example all up-regulated genes are correlated. This is not an issue. ...
written 4 days ago by Michael Love21k
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Comment: C: DeSeq2 Ribosome Profiling: multiple factor design
... For the interpretation of the coefficients, I’d recommend working with a statistician. If you take a look at the design matrix itself (plugging in to model.matrix for example), you can get an idea how the coefficients are used to explain various differences across samples. ...
written 4 days ago by Michael Love21k
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Comment: C: DeSeq2 Ribosome Profiling: multiple factor design
... I think you want a design of `~time + assay + cond + cond:assay + time:assay + time:cond + time:cond:assay`. If you arrange the colData such that the times are grouped together, it's clearer that the above design gives you a simple 2x2 interaction model for time=0, and then the other time points al ...
written 4 days ago by Michael Love21k

Latest awards to Michael Love

Teacher 6 days 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 8 days ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 9 days ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Teacher 9 days 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 10 days ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Good Answer 11 days ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Appreciated 13 days ago, created a post with more than 5 votes. For A: DESeq2 baseMean values for each sample
Scholar 13 days ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 7 weeks ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 7 weeks ago, created an answer that has been accepted. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Teacher 7 weeks 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 7 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 7 weeks 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 11 weeks ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 11 weeks ago, created an answer that has been accepted. For A: DESeq2 - Three Sample Analysis
Scholar 11 weeks ago, created an answer that has been accepted. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Scholar 11 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Teacher 11 weeks 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 11 weeks ago, created an answer that has been accepted. For A: Should I use alpine and can I convert the output back to counts?
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: How does DESeq2 handle zero counts in one condition?
Great Question 11 weeks ago, created a question with more than 5,000 views. For New function lfcShrink() in DESeq2
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: DESeq2 1.20.0 lfcshrink function
Scholar 11 weeks ago, created an answer that has been accepted. For A: DESeq2 on two groups
Prophet 11 weeks ago, created a post with more than 20 followers. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: DESeq2 why estimate dispersion on log scale

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