User: Michael Love

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Michael Love1.6k
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Posts by Michael Love

<prev • 98 results • page 1 of 10 • next >
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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 1 day ago by Michael Love1.6k
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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 8 months ago by Michael Love1.6k
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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 9 months ago by Michael Love1.6k
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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 10 months ago by Michael Love1.6k
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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 10 months ago by Michael Love1.6k
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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 11 months ago by Michael Love1.6k
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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 11 months ago by Michael Love1.6k
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Answer: A: what's the meaning of a Concordance at the Top plot(CAT plot)
... The reference points to here: http://biostats.bepress.com/jhubiostat/paper71/ At this link you can pull up the PDF and see Figure 2. In the text you have: > To account for this fact we introduce a new descriptive plot: the > correspondence at the top (CAT) plot. To create the CAT plot we r ...
written 11 months ago by Michael Love1.6k
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Answer: A: Gene Set Enrichment Analysis after DESeq2
... Here's a link to an answer I wrote a few years ago for using the gene set testing package *goseq* following *DESeq2*: https://support.bioconductor.org/p/64811/#64815 I'm not sure what kind of input GSEA takes. I also like the methods behind *ROAST* and *CAMERA* from the limma package, but I haven' ...
written 12 months ago by Michael Love1.6k
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Comment: C: Changes to dispersion estimates in DESeq2?
... At four institutes I've worked at there were multiple R versions on the cluster available via e.g. 'module load r-3.4.1' This solves most issues as then users can have Bioconductor packages in personal library locations which won't change version over time (as it's linked to the R version), unless ...
written 12 months ago by Michael Love1.6k

Latest awards to Michael Love

Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: What exactly means the Dispersion Plot DESeq2?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 12 months ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Commentator 12 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
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 14 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Popular Question 18 months ago, created a question with more than 1,000 views. For New simulation dataset for 'A benchmark for RNA-seq quantification pipelines'
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: What exactly means the Dispersion Plot DESeq2?
Supporter 2.2 years ago, voted at least 25 times.
Good Answer 2.4 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 2.5 years ago, received more than 100 upvotes.
Commentator 2.5 years ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Scholar 2.5 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Can someone please explain in simple terms how DESeq2 works?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 3.3 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis

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