User: Michael Love

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Michael Love1.5k
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Posts by Michael Love

<prev • 93 results • page 1 of 10 • next >
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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 10 days ago by Michael Love1.5k
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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 10 days ago by Michael Love1.5k
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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 4 weeks ago by Michael Love1.5k
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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 4 weeks ago by Michael Love1.5k
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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 8 weeks ago by Michael Love1.5k
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Comment: C: Different PCA plots using rlog and vsd on the same data set
... Please add links when you cross post to multiple forum sites. ...
written 8 weeks ago by Michael Love1.5k
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Comment: C: Changes to dispersion estimates in DESeq2?
... I think the relevant change was to stabilize the estimates of mu_ij that's listed in NEWS between 1.10 and 1.14. This could then have an effect downstream, modifying the dispersion estimates. I always recommend users to not switch versions once they've started an analysis and are wedded in some way ...
written 8 weeks ago by Michael Love1.5k
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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 10 weeks ago by Michael Love1.5k
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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 weeks ago by Michael Love1.5k
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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 11 weeks ago by Michael Love1.5k

Latest awards to Michael Love

Scholar 4 weeks ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 3 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Popular Question 7 months ago, created a question with more than 1,000 views. For New simulation dataset for 'A benchmark for RNA-seq quantification pipelines'
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: What exactly means the Dispersion Plot DESeq2?
Supporter 16 months ago, voted at least 25 times.
Good Answer 18 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 19 months ago, received more than 100 upvotes.
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Time course experiments in DESeq2
Scholar 19 months ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Appreciated 21 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 23 months ago, created a post with more than 5 votes. For A: DESeq2: different log2FC results when using subset of data
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Can someone please explain in simple terms how DESeq2 works?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 2.4 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 2.4 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: estimation of size factors in DESeq2 analysis
Scholar 2.4 years ago, created an answer that has been accepted. For A: estimation of size factors in DESeq2 analysis

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