User: Michael Love

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Michael Love1.9k
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Posts by Michael Love

<prev • 101 results • page 1 of 11 • next >
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Comment: C: model design in rna seq - deseq2
... Cross posted to Bioconductor https://support.bioconductor.org/p/119352/ ...
written 8 months ago by Michael Love1.9k
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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 12 months ago by Michael Love1.9k
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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 13 months ago by Michael Love1.9k
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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 14 months ago by Michael Love1.9k
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Comment: C: Deseq2 question of a single factor with 3 levels
... This post was cross posted at Bioconductor which means volunteers have to answer a question twice. https://www.biostars.org/p/294625/ ...
written 23 months ago by Michael Love1.9k
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Comment: C: Changes log2FC values of DESeq2
... This is likely it. You can look for descriptions of important user relevant changes to R packages in the NEWS file. Also, here’s a longer post on motivation for the change. https://support.bioconductor.org/p/95695/ ...
written 23 months ago by Michael Love1.9k
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Answer: A: How to import RSEM results to DESeq2 for differential analysis
... You can use tximport to import RSEM quants and then DESeqDataSetFromTximport() in DESeq2. The development version of tximport allows importing transcript-level abundances as well (previously just gene-level). ...
written 2.0 years ago by Michael Love1.9k
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Comment: C: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
... p-values are indeed hard for many to interpret. Also, for many genomics datasets, the point null of no change is trivial to reject. We try to move towards working more directly with posterior estimates of the effect size itself. ...
written 2.0 years ago by Michael Love1.9k
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Comment: C: Strange distribution of logFC
... Cross-posting is discouraged as you are asking for duplicate effort from the volunteers who answer: https://support.bioconductor.org/p/102905/ ...
written 2.1 years ago by Michael Love1.9k
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Comment: C: Zero read count with deseq2
... Cross-posting, especially without noting this, is discouraged (duplicates effort of the volunteers answering questions). https://support.bioconductor.org/p/102962/ ...
written 2.1 years ago by Michael Love1.9k

Latest awards to Michael Love

Scholar 8 months ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: What exactly means the Dispersion Plot DESeq2?
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 12 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Commentator 12 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Appreciated 12 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Centurion 12 months ago, created 100 posts.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: What exactly means the Dispersion Plot DESeq2?
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 2.0 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
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Popular Question 2.7 years ago, created a question with more than 1,000 views. For New simulation dataset for 'A benchmark for RNA-seq quantification pipelines'
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: What exactly means the Dispersion Plot DESeq2?
Supporter 3.4 years ago, voted at least 25 times.
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Can someone please explain in simple terms how DESeq2 works?
Guru 3.6 years ago, received more than 100 upvotes.

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