Moderator: Michael Love

gravatar for Michael Love
Michael Love20k
Reputation:
20,210
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
11 hours ago
Joined:
5 years, 9 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 • 4,141 results • page 1 of 415 • next >
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Comment: C: DESEq2 comparison with two conditions and paired experiments
... You are highlighting that the interaction is not significant while the main effect in the "damage" group is significant. There is nothing inconsistent here. ...
written 2 days ago by Michael Love20k
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Comment: C: DESEq2 comparison with two conditions and paired experiments
... The first procedure is a statistical test of the interaction and is the recommended test. The second is an ad-hoc procedure without FDR control on the resulting set. Sometimes intersecting FDR sets is the only option, and the resulting intersection set does not have FDR control, but here there is a ...
written 2 days ago by Michael Love20k
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Answer: A: When should I use betaprior=T
... Not really a use case. It’s obsolete except we kept it to not break old code that used it. The apeglm paper shows that the new heavy tailed methods (apeglm and ashr) outperform the Normal prior pretty much in every case. ...
written 2 days ago by Michael Love20k
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Answer: A: DGE Analysis between 3 conditions
... Yes I would approach this by just looking at the intersection of the two FDR sets. ...
written 3 days ago by Michael Love20k
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Comment: C: DESeq2 count outlier replacement from Cook's threshold
... That should work. Well hopefully have an improved method for outliers out soon next year. ...
written 3 days ago by Michael Love20k
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Answer: A: DESeq2 count outlier replacement from Cook's threshold
...  The motivation of that value for the threshold is given in the DESeq2 paper in the section that talks about outliers.  In short it means that the beta vector shouldn’t move too much with the removal of a single sample.  You can lower it globally for a particular dataset, and actually, in linear reg ...
written 4 days ago by Michael Love20k
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Comment: C: How to create tx2gene.gencode.v27.csv
... For kallisto you should build a tx2gene table, but this should be fairly easy if you know the reference you used as the index. Follow the instructions in the tximport vignette: download the v28 GTF file from Gencode, then bring this into R and use select() to create a data.frame. ...
written 4 days ago by Michael Love20k
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Comment: C: Post-hoc filtering on the standard deviation in proportions
... Yes that’s what you would do ...
written 4 days ago by Michael Love20k
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Answer: A: Post-hoc filtering on the standard deviation in proportions
... The first "rnaseqDTU" post! Yes, you should put res.txp.filt$pvalue as the single column of pConfirmation, for performing stageR adjustment on the filtered transcript results. If you want to see more of the original code it is here (with the relevant chunk highlighted): https://github.com/mikelov ...
written 4 days ago by Michael Love20k
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Comment: C: DESeq2: Error using packet 1 arguments must have same length
... You have three commented out lines. The first two are entirely different designs. If you don’t understand the difference between these you should consult a statistician. This forum is for software guidance, when users know what model they want to use.  The last commented out like won’t work. See th ...
written 4 days ago by Michael Love20k

Latest awards to Michael Love

Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: DESeq2 1.20.0 lfcshrink function
Scholar 5 weeks ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Teacher 5 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
Great Question 5 weeks ago, created a question with more than 5,000 views. For New function lfcShrink() in DESeq2
Scholar 5 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 5 weeks ago, created an answer that has been accepted. For A: DESeq2 on two groups
Prophet 5 weeks ago, created a post with more than 20 followers. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 5 weeks ago, created an answer that has been accepted. For A: DESeq2 - Three Sample Analysis
Scholar 5 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 5 weeks ago, created a post with more than 5 votes. For A: How does DESeq2 handle zero counts in one condition?
Scholar 5 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 9 weeks ago, created an answer with at least 3 up-votes. For A: What doest this p.value distribution mean?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: How does DESeq2 handle zero counts in one condition?
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2 why estimate dispersion on log scale
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2 baseMean values for each sample
Scholar 9 weeks ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 9 weeks ago, created an answer that has been accepted. For A: DESeq2 on two groups
Scholar 9 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 9 weeks ago, created an answer that has been accepted. For A: DESeq2 confounding cartridge
Scholar 9 weeks ago, created an answer that has been accepted. For A: Should I use alpine and can I convert the output back to counts?
Scholar 9 weeks ago, created an answer that has been accepted. For A: Get release date for version of DESeq2
Scholar 9 weeks ago, created an answer that has been accepted. For A: DESeq2 - Three Sample Analysis
Scholar 9 weeks ago, created an answer that has been accepted. For A: Post-processing RNA-Seq after tximport
Teacher 9 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 9 weeks ago, created an answer that has been accepted. For A: DESeq2 why estimate dispersion on log scale

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