Moderator: Michael Love

gravatar for Michael Love
Michael Love25k
Reputation:
25,260
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
3 hours ago
Joined:
6 years, 7 months ago
Email:
m****************@gmail.com

Michael I. Love, Dr. rer. nat.
Assistant Professor
Department of Biostatistics
Department of Genetics
University of North Carolina-Chapel Hill

The Love lab maintains the following R/Bioconductor packages:

the RNA-seq gene-level workflow, and the RNA-seq DTU workflow.

Posts by Michael Love

<prev • 5,177 results • page 1 of 518 • next >
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Answer: A: Biased results of DESeq2 LRT (Group name order)
... Above you have code for the Wald test, is this on purpose? Do you know that you’re doing pairwise comparisons? You should remove these lines: DESeq2Table <- estimateSizeFactors(DESeq2Table) DESeq2Table <- estimateDispersions(DESeq2Table) DESeq2Table <- nbinomWaldTest(DESeq2Table) ...
written 3 hours ago by Michael Love25k
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Comment: C: What is lfcSE and how is it calculated?
... As with your question about size factors, SE of beta (LFC) is detailed in our 2014 paper. Please check their first for method details. ...
written 8 hours ago by Michael Love25k
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Comment: C: write.table of DESeq2 results broken down by LFC
... I don't have any more or different advice for you, the above is simple and clear what's happening, right? You're better off with a few clear lines of R code than asking for some dedicated obtuse wrapper function. ...
written 10 hours ago by Michael Love25k
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Answer: A: What is lfcShrink and how is it calculated?
... Can you provide your exact code? There isn't a `res` function in DESeq2, and there isn't a column `lfcShrink` in the results table. I need to know specifically what you are referring to. Note that there is a lot of details about this in the vignette, so that would be a good place for you to start. ...
written 11 hours ago by Michael Love25k
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Comment: C: How to create manhattan plot with DESeq2
... If you want specific help, can you provide more specific information about what you have? How have you quantified gene expression? Are you using tximport/tximeta or some other counting tool? Do you already have a `DESeqDataSet` with chromosome and start position for each gene, or do you need to kn ...
written 12 hours ago by Michael Love25k
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Answer: A: How to create manhattan plot with DESeq2
... You can use this code (just modifying so the -log10 pvalue is plotted instead of the LFC). Also you'd probably not want to bother adding the genes because there will be too many. https://bioconductor.org/packages/devel/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#plotting-fold-changes-in ...
written 15 hours ago by Michael Love25k
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Comment: C: What are size factors used for in baseMean calculation
... Yes that’s definitely described in the paper also. ...
written 1 day ago by Michael Love25k
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Answer: A: What are size factors used for in baseMean calculation
... Can you take a look first at the 2014 paper? It explains in full detail these steps. ...
written 1 day ago by Michael Love25k
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Answer: A: How I deal with this expression set
... The RNAseq gene-level workflow (linked from vignette) helps users to get started from count table and sample information. Start there first, and post it you have specific questions. ...
written 1 day ago by Michael Love25k
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Answer: A: DESeq2 analysis with multiple factors
... I’d recommend speaking with a statistician about your experimental design and analysis plan. I don’t have much time to provide statistical consulting beyond the details given in the vignette. ...
written 3 days ago by Michael Love25k

Latest awards to Michael Love

Scholar 9 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 9 weeks ago, created an answer that has been accepted. For A: Multiple groups and two methods to analyse them with DESeq2
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 9 weeks ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Prophet 9 weeks ago, created a post with more than 20 followers. For New function lfcShrink() in DESeq2
Scholar 10 weeks ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
Scholar 10 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 10 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 10 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 10 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 11 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 12 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 3 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Appreciated 3 months ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 9 months ago, created an answer that has been accepted. For A: Using altHypothesis with shrunken LFC values in DESeq2
Scholar 9 months ago, created an answer that has been accepted. For A: Unable to find an inherited method for function 'results' for signature '"DESeqD
Scholar 9 months ago, created an answer that has been accepted. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Scholar 9 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 9 months ago, created an answer that has been accepted. For A: DESeq2 lfcShrink using only dds and res arguments
Scholar 9 months ago, created an answer that has been accepted. For A: Change lower bound 'optim' function in DESeq2::unmix() to 0.001 to prevent error

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