User: Michael Love

gravatar for Michael Love
Michael Love2.0k
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United States
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Joined:
6 years, 3 months ago
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Posts by Michael Love

<prev • 107 results • page 1 of 11 • next >
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Comment: C: DESeq2 analysis with covariates with and without log transformation
... I recommend to transform and scale numeric covariates (current DESeq2 will warn you about this). There is no hard-coded limitation (the program will run, with a message recommending you to scale the covariate), but if you put in highly skewed covariates that aren't scaled to a linear model, you may ...
written 24 days ago by Michael Love2.0k
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Answer: A: DESeq2 analysis with covariates with and without log transformation
... For future reference, the Bioconductor support website is: https://support.bioconductor.org It is listed from the DESeq2 vignette and the man pages. But I will reply here to make it simpler. I don't usually add these types of numeric covariates to the design with DESeq2. I will use RUV or SVA if ...
written 24 days ago by Michael Love2.0k
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Comment: C: Transcript level counts from full length scRNA data
... I like to consolidate Bioc related questions on the other support site. Feel free for anyone to post a tximport question there. ...
written 25 days ago by Michael Love2.0k
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Comment: C: DeSeq2 error: counts matrix should be numeric, currently it has mode: character
... Cross posted https://support.bioconductor.org/p/131243/ ...
written 11 weeks ago by Michael Love2.0k
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Comment: C: When should one be concerned about the CG content in RNA-seq experiment?
... Note, you are plotting the GC content of the **genome** and for **mouse**. You can use the theoretical GC content customization in MultiQC to instead plot the GC content of the human transcripts: https://multiqc.info/docs/#theoretical-gc-content ...
written 3 months ago by Michael Love2.0k
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Answer: C: Is a simple Wilcoxon rank sum test good enough to identify differentially expres
... I agree with Devon here except I'd put the number even lower than 100 for trusting Wilcoxon. Rank based tests will find differences with sufficient power once you have, say dozens of cells with non-zero counts in each group that you want to compare. We used Wilcoxon tests with Gibbs samples to also ...
written 5 months ago by Michael Love2.0k
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Comment: C: model design in rna seq - deseq2
... Cross posted to Bioconductor https://support.bioconductor.org/p/119352/ ...
written 16 months ago by Michael Love2.0k
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Comment: C: How is the design in DESeq2 work?
... Just posted this on twitter, but cross-posting here too: The syntax is originally from here: https://www.jstor.org/stable/2346786?seq=1#metadata_info_tab_contents It is sometimes called Wilkinson (& Rogers) syntax. In the vignette, there are diagrams on interpreting [interactions][1]. A brief ...
written 20 months ago by Michael Love2.0k
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Comment: C: Pair-wise DESeq Analysis with 3 Factor Levels - RNA-Seq
... Please note the cross post on both sites: https://support.bioconductor.org/p/115065/ ...
written 21 months ago by Michael Love2.0k
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Answer: A: "Duplicate rownames not allowed" when the rownames are not duplicated
... To propagate the answer from Bioconductor support site back here: > The problem is that you have duplicate columns of colData(dds), which > breaks some code where replaceOutliers adds a column to colData(dds) > and adds some metadata about that column. > > `sum(duplicated(colnames(c ...
written 22 months ago by Michael Love2.0k

Latest awards to Michael Love

Scholar 9 weeks ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Commentator 9 weeks ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Scholar 11 weeks ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 16 months ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Good Answer 20 months ago, created an answer that was upvoted at least 5 times. For A: What exactly means the Dispersion Plot DESeq2?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Appreciated 20 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Appreciated 20 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Centurion 20 months ago, created 100 posts.
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: What exactly means the Dispersion Plot DESeq2?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 2.8 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Popular Question 3.3 years ago, created a question with more than 1,000 views. For New simulation dataset for 'A benchmark for RNA-seq quantification pipelines'

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