Moderator: Michael Love

gravatar for Michael Love
Michael Love26k
Reputation:
25,520
Status:
Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Scholar ID:
Google Scholar Page
Last seen:
9 hours ago
Joined:
6 years, 8 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 • 5,235 results • page 1 of 524 • next >
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Comment: C: Cannot find header.json in salmon index directory
... BTW, if I push a fix today, it should show up in the release branch by noon tomorrow (or the next day if something goes wrong). ...
written 9 hours ago by Michael Love26k
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Comment: C: Cannot find header.json in salmon index directory
... Thanks for the bug report. I'll push a fix to the release branch today. The information has moved as you said from header.json to info.json in the index and so I'll just need a line to check both places. ...
written 9 hours ago by Michael Love26k
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Answer: A: same results changing contrast function
... You can use triple backticks (`) to make code blocks, I've edited your post. If you change the order of the two levels in the contrast, the only thing that will change is the LFC and t-statistic. Check over your code very carefully if you think otherwise. Just do: ``` results(dds, contrast=c("cond ...
written 10 hours ago by Michael Love26k
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Comment: C: Analyse Mircoarray Data - AVG_Signal
... Correct. DESeq2 is not appropriate for microarray. ...
written 10 hours ago by Michael Love26k
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Answer: A: How to handle batch effect and interaction with experimental variables
... This appears to be a question about the linear modeling, and you have a very complex dataset with many analysis choices. I would highly recommend working with a statistician on this design and analysis plan. I don't have time to provide non-software related questions on the site at this time. ...
written 10 hours ago by Michael Love26k
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Comment: C: DESEq2 comparison with two conditions and paired experiments
... This is a complex design and there are many choices to work through. I'd recommend working with a statistician. I just don't have time to provide non-software related support here. ...
written 10 hours ago by Michael Love26k
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Answer: A: Cannot find header.json in salmon index directory
... What version of Salmon are you using? ...
written 13 hours ago by Michael Love26k
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Comment: C: DESeq2 likelihood ratio test (LRT) design
... I'd recommend meeting with a statistician to further understand how various designs work. My time on the support site is really designed for software support, not statistical analysis or experimental design consultation. ...
written 1 day ago by Michael Love26k
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Comment: C: U-shape of p-value histograms is removed by filtering for genes that have >5 cou
... One aspect is that this would likely be filtered for Cook's distance outliers except filtering here isn't possible because of the continuous covariate you're using. I don't typically use RIN in the design formula, I prefer using a method like RUV or SVA (see workflow for code). But can you try again ...
written 1 day ago by Michael Love26k
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Comment: C: DESeq2 paired multifactor test
... The difference between those terms is subtle and I’d recommend working with a statistician that can walk you through it. ...
written 1 day ago by Michael Love26k

Latest awards to Michael Love

Scholar 12 weeks ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 12 weeks ago, created an answer that has been accepted. For A: Multiple groups and two methods to analyse them with DESeq2
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 12 weeks ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Prophet 3 months ago, created a post with more than 20 followers. For New function lfcShrink() in DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: Correlation of gene expression values using tpms and normalized counts
Scholar 3 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 3 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Popular Question 3 months ago, created a question with more than 1,000 views. For Updated DESeq2 performance on highly replicated yeast RNA-seq data
Scholar 3 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 3 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 3 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 3 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Scholar 3 months ago, created an answer that has been accepted. For A: difference among tximport scaledTPM, lengthScaledTPM and the original TPM output
Appreciated 4 months ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 10 months ago, created an answer that has been accepted. For A: Using altHypothesis with shrunken LFC values in DESeq2
Scholar 10 months ago, created an answer that has been accepted. For A: Unable to find an inherited method for function 'results' for signature '"DESeqD
Scholar 10 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 10 months ago, created an answer that has been accepted. For A: One-sided p-value from DESeq2
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2 lfcShrink using only dds and res arguments
Scholar 10 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

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