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Moderator: Michael Love

gravatar for Michael Love
Michael Love21k
Reputation:
21,450
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
8 hours ago
Joined:
5 years, 11 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 • 4,384 results • page 1 of 439 • next >
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Comment: C: DESeq2 overestimates log2Fold Change
... Right, so the LFC is not an average over an average for this design, even if you were doing simple linear regression on log counts. ...
written 2 days ago by Michael Love21k
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Answer: A: tximport: question concerning 'bias corrected counts without an offset' method
... Just round() the counts before passing to DESeqDataSetFromMatrix(). ...
written 2 days ago by Michael Love21k
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Answer: A: Data filtering in DESeq2
... It depends on the data of course. I never claimed the filtering _only_ affects the speed, but I said that this and the reduced memory size of the object make some pre-filtering useful for most datasets. If you have found that pre-filtering provides better results on your dataset, that is of course ...
written 2 days ago by Michael Love21k
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Comment: C: DESeq2 overestimates log2Fold Change
... Thanks James, I would just add that we don't even know the design as its not included above. As, James points out, the design is critical in fitting the coefficients, and only in a subset of designs is looking at ratios of average of norm. counts relevant. ...
written 2 days ago by Michael Love21k
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Comment: C: LRT test followed by filtering based on LFC
... You can pull out the LFCs for individual coefficients that are dropped in the LRT, and then do simple filtering in R, right? Like you said, we don’t have any kind of combination lfcThresholding on multiple coefficients at once. Another way to go would be to use lfcThreshold and Wald tests and combin ...
written 2 days ago by Michael Love21k
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Answer: A: LRT test followed by filtering based on LFC
... You want just the LFC for each of the coefficients? See the vignette on “Access to all calculated values” or ?results on the LRT test. ...
written 2 days ago by Michael Love21k
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Answer: A: Summary results interpretation in DeSeq2
... The outliers and low counts have been removed from the FDR bounded set, by setting padj to NA (see vignette). So you don’t have to do anything. ...
written 2 days ago by Michael Love21k
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Answer: A: DESeq2:varianceStabilizingTransformation suggested. Results suspicious
... What kind of samples do you have? How many? That warning is flagged for extremely sparse data. I wrote it to be self explanatory, that you have a lot of genes where most of the row count comes from a single sample. ...
written 2 days ago by Michael Love21k
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Comment: C: DESeq2: 5 Conditions (B vs C) vs (D vs B)
... Sorry I mistyped above. To get a one sided test, above 1 or below -1, you should do `lfcThreshold=1` and `altHypothesis="greaterAbs"` or `altHypothesis="lessAbs"`. You can use a numeric contrast, but it's safer to use the code I had above, because it will always be correct even if you happened to re ...
written 3 days ago by Michael Love21k
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Comment: C: DESeq2: paired samples + controls
... In this design it just adds no information. I don’t think it produces any problem for the inference. I know this is the case for linear modeling at least. ...
written 3 days ago by Michael Love21k

Latest awards to Michael Love

Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Scholar 5 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 5 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Scholar 5 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. 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 A: DESeq2 baseMean values for each sample
Scholar 5 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 10 weeks ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Scholar 10 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 10 weeks 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 3 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: DESeq2 - Three Sample Analysis
Scholar 3 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 3 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to set up appropriate analysis using sample type and condition for DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: Should I use alpine and can I convert the output back to counts?
Appreciated 3 months ago, created a post with more than 5 votes. For A: How does DESeq2 handle zero counts in one condition?
Great Question 3 months ago, created a question with more than 5,000 views. For New function lfcShrink() in DESeq2
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 1.20.0 lfcshrink function
Scholar 3 months ago, created an answer that has been accepted. For A: DESeq2 on two groups
Prophet 3 months ago, created a post with more than 20 followers. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: DESeq2 why estimate dispersion on log scale

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