Moderator: Michael Love

gravatar for Michael Love
Michael Love25k
Reputation:
24,850
Status:
Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
26 minutes ago
Joined:
6 years, 6 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 • 5,092 results • page 2 of 510 • next >
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Answer: A: 51 views DESeq2 RNAseq differential expression analysis
... You can remove as many coefficients as you want. This is up to you as the analyst. You can either provide a reduced design formula, as above, or you can provide model matrices directly: ``` dds <- DESeq(dds, test="LRT", full=mm, reduced=mm0) ``` Where `mm` and `mm0` are created by `model.matr ...
written 9 hours ago by Michael Love25k
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Comment: C: Responder Vs Non-Responders Paired Comparison DESeq2
... Either way is fine. When you relevel the column of the DESeqDataSet, you haven’t modified the sampleTable obviously. R doesn’t back propagate your changes to objects used to construct dds. ...
written 1 day ago by Michael Love25k
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Comment: C: Responder Vs Non-Responders Paired Comparison DESeq2
... The top code doesn't work because you create `model` from `sampleTable` which has the wrong coding. ...
written 1 day ago by Michael Love25k
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Answer: A: Responder Vs Non-Responders Paired Comparison DESeq2
... https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#note-on-factor-levels ...
written 1 day ago by Michael Love25k
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Comment: C: Silent error in tximport after upgrade to R 3.6.1
... GEOquery installs readr (it is an import) and that changes tximport’s behavior. So it seems like readr is the potentially culprit on your machine (that it exits silently). You can override by setting importer=read.delim when you run tximport(). ...
written 6 days ago by Michael Love25k
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Answer: A: DESeq2 RNAseq differential expression analysis
... I feel like this is already answered in the manual: 1) provide un-normalized counts to DESeq2 2) for details on how the method works, read the publication ...
written 6 days ago by Michael Love25k
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Comment: C: Subset-ing Large DESeqDataSet for data extraction with contrast function
... Your first step should be looking up help for functions. ?results See BPPARAM Also if you want to keep going with DESeq2, go ahead and use the development branch which is 10x faster for this size of dataset. That’s more than you’ll get with parallelization. ...
written 6 days ago by Michael Love25k
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Comment: C: Subset-ing Large DESeqDataSet for data extraction with contrast function
... Yes the second is what I’m recommending. ...
written 6 days ago by Michael Love25k
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Answer: A: FPM value and batch correction
... Agree with Gordon that you are mixing various pipelines. As in the DESeq2 vignette if you want to remove batch effect variation for heatmaps etc, we recommend to do so on log scale data, so using vst() first. See the FAQ in our vignette. ...
written 6 days ago by Michael Love25k
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Comment: C: Silent error in tximport after upgrade to R 3.6.1
... No, no changes to this basic functionality. Can you try on another machine, and if this works, I’d recommend reinstalling your packages. ...
written 7 days ago by Michael Love25k

Latest awards to Michael Love

Scholar 4 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 4 weeks ago, created an answer that has been accepted. For A: Multiple groups and two methods to analyse them with DESeq2
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 4 weeks ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
Good Answer 4 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 4 weeks ago, created a post with more than 20 followers. For New function lfcShrink() in DESeq2
Scholar 5 weeks ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
Scholar 5 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 5 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Teacher 5 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 5 weeks ago, created a question with more than 1,000 views. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 5 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 6 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Good Answer 6 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 6 weeks ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 7 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 7 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 8 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Appreciated 9 weeks ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 8 months ago, created an answer that has been accepted. For A: Using altHypothesis with shrunken LFC values in DESeq2
Scholar 8 months ago, created an answer that has been accepted. For A: Unable to find an inherited method for function 'results' for signature '"DESeqD
Scholar 8 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 8 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 8 months ago, created an answer that has been accepted. For A: DESeq2 lfcShrink using only dds and res arguments
Scholar 8 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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