Moderator: Michael Love

gravatar for Michael Love
Michael Love22k
Reputation:
21,920
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
40 minutes ago
Joined:
6 years 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 • 4,514 results • page 2 of 452 • next >
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Answer: A: Vertical line at A=0, nothing else, on MA plot
... First, I think you probably want to swap the order of the second and third arguments, if you want 653 / Control. See `?results` Can you print res, like so: ``` res ``` And copy here what the output is? ...
written 4 days ago by Michael Love22k
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Comment: C: Phyloseq to deseq2
... You can use ~1 as long as you change the design later to the appropriate one with design(dds) <- ... ...
written 4 days ago by Michael Love22k
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Answer: A: Finding genes that are expressed only in one condition within a contrast
... We don’t have a way in DESeq2 to determine what counts or TPM correspond to “expressed” and what to “not expressed”. When students or collaborators want to do this I typically recommend looking at histsograms of abundance (TPM) over all genes. ...
written 4 days ago by Michael Love22k
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Comment: C: DESEQ2 - help with interpreting time series heatmaps and resultsName
... I think you’d be better off meeting with a statistician to discuss how interactions work in a linear model. I try to provide software support here on the support site, but I don’t really have time to provide extended statistical and analysis support. For this you should really find a statistical or ...
written 4 days ago by Michael Love22k
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Comment: C: Phyloseq to deseq2
... It looks like you are not following my advice above about using contrast. Please read over the documentation about using “contrast” in the vignette and in ?results ...
written 4 days ago by Michael Love22k
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Comment: C: Normalisation for count data visualisation only
... They are all scaled to have sum of one million. I have in the past done extra scaling of TPM using the media ratio method to remove additional global differences which then produces sums that are not equal to one million but tend to minimize changes for more genes. This is up to you. Most just use T ...
written 5 days ago by Michael Love22k
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Answer: A: Multiple comparisons with Deseq2
... If you have questions about how a particular function works in R, the best way to go is look up the help page for that function: `?results` And see the contrast argument in particular. Also this is discussed in the vignette. ...
written 5 days ago by Michael Love22k
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Comment: C: Phyloseq to deseq2
... Usually these messages can be ignored when they involve one or two genes and usually these genes have some outlier counts. ...
written 5 days ago by Michael Love22k
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Answer: A: DESeq2 coldata and count data subset
... I don’t see any particular problem with your code, for an analysis where you expect one group behaves differently from other groups which can be put together for the purposes of finding consistent differences. If I were you I would make plots for the genes you expect to be DE. ...
written 6 days ago by Michael Love22k
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Answer: A: randomized design (Treatment and time)
... Yes this design will pull out the differences over time, controlling for the difference at base line, while also each subject has their own placebo baseline. ...
written 6 days ago by Michael Love22k

Latest awards to Michael Love

Teacher 9 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 9 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Scholar 9 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Teacher 9 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 9 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Good Answer 9 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 9 weeks ago, created a post with more than 5 votes. For A: DESeq2 baseMean values for each sample
Scholar 9 weeks ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
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: How to set up appropriate analysis using sample type and condition for 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: ntop parameter in plotPCA(). DESeq2
Scholar 3 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 4 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 4 months ago, created an answer that has been accepted. For A: DESeq2 - Three Sample Analysis
Scholar 4 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 4 months ago, created an answer that has been accepted. For A: ntop parameter in plotPCA(). DESeq2
Teacher 4 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 4 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 4 months ago, created a post with more than 5 votes. For A: How does DESeq2 handle zero counts in one condition?
Great Question 4 months ago, created a question with more than 5,000 views. For New function lfcShrink() in DESeq2
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 1.20.0 lfcshrink function
Scholar 4 months ago, created an answer that has been accepted. For A: DESeq2 on two groups
Prophet 4 months ago, created a post with more than 20 followers. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: DESeq2 why estimate dispersion on log scale

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