Moderator: Michael Love

gravatar for Michael Love
Michael Love19k
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18,670
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Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
3 days, 9 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 2 of 377 • next >
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Answer: A: DESeq2: likelihood ratio test interpretation, multifactor
... "I understand that the likelihood ratio test is testing whether the reduced model (dispersions estimated on sex alone) or the full model (dispersions estimated on sex and condition) better fits the dataset." Close, but not exactly. It tests whether the increase in the log likelihood from the additi ...
written 4 days ago by Michael Love19k
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Answer: A: Changes in DESeq2 Version 1.20?
... I didn't see this because the 'deseq2' tag wasn't used. Are you using a cluster? Likely what happened is that someone update the version of R and Bioconductor, switching you from a previous version to the current version. The estimate of LFC that DESeq() and results() gives you hasn't changed sinc ...
written 4 days ago by Michael Love19k
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Comment: C: Strange results from Deseq2
...  There may be genes that you’re missing with low count, and you could turn off independent filtering to try to capture these, but you’ll end up with less differentially expresses genes in total (because that’s how the independent filter works, see the diagram in vignette). ...
written 5 days ago by Michael Love19k
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Answer: A: DESeq2 relevel still gives negative log2FoldChange
... What do you want to be the denominator of the contrast? Can you look over the description of the ‘contrast’ argument in ?results ...
written 5 days ago by Michael Love19k
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Answer: A: Strange results from Deseq2
...  The threshold that is chosen by independent filtering depends on whether greater power can it be achieved by increasing the threshold. It needs to be the case that there are alternative hypotheses with sufficient power at higher counts, and that filtering out lower count rows helps to make these di ...
written 5 days ago by Michael Love19k
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Answer: A: Seurat/DESeq2 - single cell RNA-seq differential expression
...   As to speed, DESeq2 will be a lot slower than say a linear model when you have thousands of replicates. The software wasn’t optimized for this use case. According to a recent paper from Soneson and Robinson, you can use Wilcoxon effectively here for DE. If you want to compare hundreds of cells w ...
written 5 days ago by Michael Love19k
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Answer: A: DESeq2 - Three Sample Analysis
... DESeq2 doesn't offer null hypothesis testing for single replicate data. You can create a DESeqDataSet with a design of ~1, and then you can compute the vst(), and make plots using the variance stabilized data (so, yes, you're stuck with just EDA). It's not possible to perform differential expression ...
written 5 days ago by Michael Love19k
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Answer: A: DESeq2 on two groups
... Is there additionally batch information? It looks like the right group is split 3/3, 3/3/ and 2/4 by something other than what you've got being used to color now. If you suspect batches, you could use sva or RUVSeq to identify them. See the last section of our workflow. If not, then yes, I'd recom ...
written 5 days ago by Michael Love19k
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Comment: C: Error DESeq2 plotCounts invalid class DESeqDataSet object undefined class for sl
... This is the problem then. The update object methods for a SummerizedExperiment isn’t working. This is outside the scope of what I can fix in DESeq2. But to help you fix things, can you rebuild the object from counts and sample table? ...
written 5 days ago by Michael Love19k
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Answer: A: Error DESeq2 plotCounts invalid class DESeqDataSet object undefined class for sl
... Critical to what's going on is that you likely switched versions of software between object creation and the latest time you tried to run the code. This could be because you are working on a cluster and R/Bioconductor were updated, or you did this on your own machine. As with all support site posts, ...
written 6 days 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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