Moderator: Michael Love

gravatar for Michael Love
Michael Love19k
Reputation:
18,640
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
16 hours ago
Joined:
5 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:

and the RNA-seq gene-level workflow.

Posts by Michael Love

<prev • 3,769 results • page 1 of 377 • next >
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Comment: C: ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like t
... At Bioc2018, someone was saying that UMI counts might not require zero-inflated component, but I forget who said this and what was the evidence or paper that backed it up. ...
written 16 hours ago by Michael Love19k
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Answer: A: ZINB-WaVE + DESeq2 misses low-expressed, single-condition genes that look like t
... hi Rory, Thanks, this is really interesting. It's funny from dataset to dataset, and depending on application, these kinds of rows will either be desired to be detected or not detected. The other week someone was saying that DESeq2 was too sensitive to DE when it was only a subset of samples (but ...
written 16 hours ago by Michael Love19k
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Comment: C: Using DESeq2 for T-cell receptor clonotypes
... That's what i recommended above ...
written 21 hours ago by Michael Love19k
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Comment: C: Using DESeq2 for T-cell receptor clonotypes
... That looks fine. The overall range really isn’t so bad. ...
written 23 hours ago by Michael Love19k
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Answer: A: Using DESeq2 for T-cell receptor clonotypes
... I think the dispersion shrinkage can be useful even with eg 100 rows. The depth issue is not a problem alone, unless it is very confounded with condition. Can you plot sizeFactors(dds) over dds$condition? With so few genes you may want to use fitType=“mean”. ...
written 23 hours ago by Michael Love19k
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Comment: C: DESeq2 multifactor design, interpreting interaction names
... In the new design each of the interaction terms is the male versus female difference for that treatment group. ...
written 1 day ago by Michael Love19k
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Answer: A: Time Series Analysis
... Your first reduced design above, where you remove treatment as well as its interaction with time in the reduced model, is testing if there is any effect of treatment at any time point include time=0. In the time series example in the workflow, we include the effect of treatment as time=0 to control ...
written 1 day ago by Michael Love19k
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Answer: A: DESeq2 multifactor design, interpreting interaction names
... You can use an alternate design which will make it easier for you to find the contrasts. Try ~treatment + treatment:gender ...
written 1 day ago by Michael Love19k
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Answer: A: DESeq2 with HTSeq DESeqDataSetFromHTSeqCount
... The contrast doesn’t appear because one can only fit the two comparisons to the reference, and additional coefficients would lead to linear dependence. In the vignette we have some simple code for running nbinomWaldTest one more time to generate the LFC and SE needed for apeglm. Can you try this co ...
written 1 day ago by Michael Love19k
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Comment: C: For multiple level variables, different results with or without subsetting
... This is also one of the FAQ in the vignette. ...
written 1 day ago by Michael Love19k

Latest awards to Michael Love

Great Question 11 weeks ago, created a question with more than 5,000 views. For New function lfcShrink() in DESeq2
Scholar 11 weeks ago, created an answer that has been accepted. For A: Should I use alpine and can I convert the output back to counts?
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: DESeq2 1.20.0 lfcshrink function
Scholar 11 weeks ago, created an answer that has been accepted. For A: Add new columns to DESeqResults from text file by matching rownames.
Scholar 11 weeks ago, created an answer that has been accepted. For A: Get release date for version of DESeq2
Scholar 11 weeks ago, created an answer that has been accepted. For A: Analysis guidance for data inclusion in deseq2 analysis: data subsets vs contras
Popular Question 11 weeks ago, created a question with more than 1,000 views. For DESeq2: Error from the generic function 'plotMA' defined in package 'BiocGenerics'
Popular Question 11 weeks ago, created a question with more than 1,000 views. For DESeq2 - experimental design
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: [DESEQ2] How to access the normalized data of a DESeqDataSet
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: How does DESeq2 handle zero counts in one condition?
Scholar 11 weeks ago, created an answer that has been accepted. For A: Unexpected differences in results from paired analysis with DESeq2
Scholar 11 weeks ago, created an answer that has been accepted. For A: DESeq2 why estimate dispersion on log scale
Scholar 11 weeks ago, created an answer that has been accepted. For A: DESeq2 confounding cartridge
Scholar 11 weeks ago, created an answer that has been accepted. For A: Post-processing RNA-Seq after tximport
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: calculate foldchange after rlogTransformation
Scholar 11 weeks ago, created an answer that has been accepted. For A: DESEQ2 design with multiple conditions
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Cross-species RNA-seq with DESeq2
Popular Question 11 weeks ago, created a question with more than 1,000 views. For DESeq2 Regularised Log for Clustering of Genes
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2 - Acquiring batch-corrected values for PCA and hierarchical clustering
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Add new columns to DESeqResults from text file by matching rownames.
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: What doest this p.value distribution mean?
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2 why estimate dispersion on log scale
Scholar 11 weeks ago, created an answer that has been accepted. For A: Age covariate continuous vs. categorical
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: DESeq2 1.20.0 lfcshrink function
Appreciated 11 weeks ago, created a post with more than 5 votes. For New function lfcShrink() in DESeq2

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