User: Michael Love

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Michael Love1.4k
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Posts by Michael Love

<prev • 86 results • page 1 of 9 • next >
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Comment: C: Efficient way to run a DESeq2 analysis with many design formulae
... Yes you don't need to re estimate ...
written 9 days ago by Michael Love1.4k
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Comment: C: Efficient way to run a DESeq2 analysis with many design formulae
... Also, from this preprint: http://www.biorxiv.org/content/early/2017/06/30/157982 We found that estimateSizeFactors() with type="poscounts" is better than the default size factor estimation when there are many zeros. So just run that before DESeq(), and it won't re-estimate size factors. (That pap ...
written 10 days ago by Michael Love1.4k
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Answer: A: Efficient way to run a DESeq2 analysis with many design formulae
... hi cdiener! Dispersion estimation does depend on the design, but size factors do not. ...
written 13 days ago by Michael Love1.4k
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Comment: C: Why DESeq2 in parallel mode is slower than normal?!
... So the overhead of simply calling 28 workers keeps you away from achieving a speedup of 28, instead you get a speedup of 8 for the toy example of sleeping for five seconds. This might be ameliorated as the task time increases, but with real data you also have to split up the data and send to each wo ...
written 3 months ago by Michael Love1.4k
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Answer: A: Why DESeq2 in parallel mode is slower than normal?!
... Can you test to see that your parallel setup is ok? For example: > register(SerialParam()) > system.time({ bplapply(1:4, function(i) Sys.sleep(5)) }) user system elapsed 0.016 0.004 20.020 > register(MulticoreParam(workers=4)) !> system.time({ bplap ...
written 3 months ago by Michael Love1.4k
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Comment: C: Verification of Global Reduction of Epigenetic Factors ?
... Linking to the question posted on Bioconductor support: https://support.bioconductor.org/p/96381/#96405 ...
written 3 months ago by Michael Love1.4k
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Comment: C: Is the VST implemented in DESeq useful on time-series cell differentiation datas
... Cross posted: https://support.bioconductor.org/p/94917/ ...
written 5 months ago by Michael Love1.4k
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Answer: A: How to define a non differentially expressed gene?
... We discuss this in the DESeq2 paper and software vignette, you can use altHypothesis="lessAbs" in which the alternative hypothesis is that |beta| < lfcThreshold. We don't perform testing on the full null region, but substitute with a test at the boundary, and return the maximum p-value of the upp ...
written 5 months ago by Michael Love1.4k
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Comment: C: What problem does the MA plot diagnose? And how do you solve it?
... The median ratio or TMM assumption for normalization is not that the majority of genes have LFC=0, but that the median or trimmed mean of ratios captures the technical shifts in counts. So it's more about the reliability of the center of the distribution of LFCs to capture technical shifts rather th ...
written 6 months ago by Michael Love1.4k
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Answer: A: DESeq2 - how to build design for multiple paired samples before/after with 2 con
... I prefer to answer DESeq2 questions on the official Bioconductor software support site, because this is where I tell users to look to see if we've answered similar questions already. It's in the documentation, etc. support.bioconductor.org Would you mind re-posting there, and can you rename the va ...
written 7 months ago by Michael Love1.4k

Latest awards to Michael Love

Teacher 10 days ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Popular Question 5 months ago, created a question with more than 1,000 views. For New simulation dataset for 'A benchmark for RNA-seq quantification pipelines'
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What exactly means the Dispersion Plot DESeq2?
Supporter 14 months ago, voted at least 25 times.
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Can someone please explain in simple terms how DESeq2 works?
Guru 16 months ago, received more than 100 upvotes.
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Scholar 17 months ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Appreciated 19 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 20 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: Can someone please explain in simple terms how DESeq2 works?
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 2.2 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 2.2 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 2.2 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Can someone please explain in simple terms how DESeq2 works?
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: Can someone please explain in simple terms how DESeq2 works?

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