Moderator: Michael Love

gravatar for Michael Love
Michael Love25k
Reputation:
24,510
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
5 hours ago
Joined:
6 years, 5 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 • 5,033 results • page 1 of 504 • next >
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Answer: A: DESeq2 heatmap and rlog transformed values
... Take a look at the text that starts here https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#exploratory-analysis-and-visualization Also the text starting here https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#data-t ...
written 11 hours ago by Michael Love25k
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Comment: C: [DESEQ2] How to access the normalized data of a DESeqDataSet
... They are scaled in such a way that any biases across samples related to isoform switching are removed. But they do not have the typical "normalization for gene length" applied, in that longer genes will have larger values in the matrix you obtain. E.g. if a gene has length L and another with length ...
written 1 day ago by Michael Love25k
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Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... You shouldn't use vst() for DE. Why don't you try following our workflow? https://www.bioconductor.org/packages/release/workflows/html/rnaseqGene.html And if you encounter problems, please make a new post with your entire code and the error that occurred if you encounter an error. ...
written 1 day ago by Michael Love25k
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Answer: A: Phyloseq to DESeq2 Help
... This is a phyloseq issue, as you haven't gotten the data into DESeq2 yet. Try making a new post (use backticks as Mike Smith suggests also for code) and tagging that package instead of DESeq2 to notify the appropriate package maintainers. ...
written 1 day ago by Michael Love25k
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Comment: C: What causes this DESeq2 error at "fitting model and testing"?
... I don't see how this is related to the thread you are adding to. A few points: vst() requires dispersion estimation. Either it has already been run and will be used by the function (if blind=FALSE), or it will run dispersion estimation internally. You can run vst() on any DESeqDataSet. Please see ...
written 2 days ago by Michael Love25k
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Answer: A: DESeq2 s-value threshold for FSOS events
... Good question. I’d say roughly the same values make sense though. When setting a threshold and calculating FSOS posterior probabilities, you are being more conservative about what should come through as a “discovery” in the final list. Bounding the aggregate rate at say 1% should give many large eff ...
written 2 days ago by Michael Love25k
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Comment: C: DESeq2 one group vs multiple groups comparison in presence of batch effect
... If you use the code I suggested, it doesn't matter what the reference level is, all levels will be present in the resultsNames(dds). ...
written 3 days ago by Michael Love25k
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Answer: A: DESeq2: Paired multifactor test with batch effect - one or more variables in des
... I can't easily see what's going on in the colData, but if you are comparing patients to their own baseline and those are nested within batch, you don't need to add `batch`. You've already done the controlling when you compare to their own baseline. Likewise, when patients are compared to their own b ...
written 3 days ago by Michael Love25k
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Comment: C: DESeq2 logfoldchange and interaction in model
... That's not correct. It performs an addition if you do `list( c("x", "y") )`, but not if you do `list("x", "y")`. ...
written 3 days ago by Michael Love25k
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Comment: C: DESeq2 normalization vs VST vs rlog
... I think it’s pretty clear from documentation that this gives counts divided by size factors. So, no, it is not log2 transforming and there is in fact a separate function for producing log2 transformed counts... I do not recommend clustering untransformed data. There was a recent post about this on ...
written 3 days ago by Michael Love25k

Latest awards to Michael Love

Good Answer 11 days ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Prophet 11 days ago, created a post with more than 20 followers. For New function lfcShrink() in DESeq2
Scholar 12 days ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
Scholar 12 days ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 12 days ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Popular Question 12 days ago, created a question with more than 1,000 views. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 17 days ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 18 days ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Good Answer 22 days ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Teacher 23 days ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 25 days 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: 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
Appreciated 5 weeks ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 7 months ago, created an answer that has been accepted. For A: Using altHypothesis with shrunken LFC values in DESeq2
Scholar 7 months ago, created an answer that has been accepted. For A: Unable to find an inherited method for function 'results' for signature '"DESeqD
Scholar 7 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 7 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 7 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
Scholar 7 months ago, created an answer that has been accepted. For A: What is the biological meaning of genes with FC = 0 after shrinkage
Scholar 7 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 7 months ago, created an answer that has been accepted. For A: DESeq2 lfcShrink using only dds and res arguments
Scholar 7 months ago, created an answer that has been accepted. For A: How to extract factor levels of coldata from deseq object?
Scholar 7 months ago, created an answer that has been accepted. For A: DESeq2::sizeFactors() function does not output the sizeFactor table.

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