Moderator: Michael Love

gravatar for Michael Love
Michael Love11k
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Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
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Joined:
4 years ago
Email:
m****************@gmail.com

Michael I. Love, Dr. rer. nat.
Assistant Professor
Departments of Biostatistics and Genetics
University of North Carolina-Chapel Hill

My main Bioconductor involvement is to maintain these software packages

and the RNA-seq gene-level workflow.

Posts by Michael Love

<prev • 2,015 results • page 1 of 202 • next >
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Comment: C: About experimental design of RNA-seq
... hi, If you have a DESeq2 specific question, feel free to make a new post. I'm removing the DESeq2 tag from this post. ...
written 12 hours ago by Michael Love11k
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Answer: A: DESeq for paired samples from different time stamps
... Can you describe what is the "condition" here? ...
written 12 hours ago by Michael Love11k
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Comment: C: Can I add subject level effect in DESeq2 and pull the correct contrast?
... I can't really follow this code, but you can use a numeric contrast to average multiple terms, if you don't want to have separate results tables. ...
written 2 days ago by Michael Love11k
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Comment: C: Can I add subject level effect in DESeq2 and pull the correct contrast?
... Personally, I would prefer to see the results separately, but if you wanted to have an "average" of the comparison, you can use numeric contrasts to average multiple coefficients. ...
written 2 days ago by Michael Love11k
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Comment: C: DESeq2 design question - Two group treatment differences accounting for response
... After recoding the `treatment` variable, yes. From scanning, I think it's just one interaction that will have no samples to fit it, but you'll want to take a look at the model matrix. ...
written 5 days ago by Michael Love11k
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Comment: C: DESeq2 design question - Two group treatment differences accounting for response
... Hmm, there is a bit of an issue here in splitting the samples based on a random effect. I see what you want to do though. I mean a practical approach, not dealing with the random effect problem, would be to have treatment with levels: control, trt1no, trt1yes, trt2no, trt2yes. There will be some fix ...
written 6 days ago by Michael Love11k
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Answer: A: DESeq2 design question - Two group treatment differences accounting for response
... And to clarify, do you determine the responder status using the RNA-seq data? ...
written 6 days ago by Michael Love11k
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Comment: C: [DESeq2] Multi-factor designs
... hi, I'd recommend you speak with a local statistician to discuss the interpretation of coefficients and how to pull out your comparisons of interest. There are many possible designs to use here, and the modeling choices are up to really. ...
written 6 days ago by Michael Love11k
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Comment: C: DESeq2 Following RSEM
... So this is a little sub-optimal compared to using tximport (which leverages the effective length information and isoform abundance estimates), but you can round the matrix of estimated counts (note, these are not normalized counts) and feed these into DESeqDataSetFromMatrix. ...
written 6 days ago by Michael Love11k
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Answer: A: Different results using DESeq2
... That would result in different parameters and inference yes. I don't know how Trinity calls DESeq2. ...
written 7 days ago by Michael Love11k

Latest awards to Michael Love

Scholar 21 days ago, created an answer that has been accepted. For A: trouble installing DESeq2
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: DESeq2 paired multifactor test
Scholar 21 days ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Teacher 22 days ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Scholar 24 days ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Scholar 26 days ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 28 days ago, created an answer that has been accepted. For A: ABOUT TRANSFORMATION OF RNA-SEQ DATA FOR GLMNET COX SURVIVAL ANALYSIS
Scholar 4 weeks ago, created an answer that has been accepted. For A: trouble installing DESeq2
Popular Question 4 weeks ago, created a question with more than 1,000 views. For DESeq2: Error from the generic function 'plotMA' defined in package 'BiocGenerics'
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Scholar 4 weeks ago, created an answer that has been accepted. For A: trouble installing DESeq2
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Scholar 5 weeks ago, created an answer that has been accepted. For A: trouble installing DESeq2
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: DESeq2: multiple conditions design -- How to select subset comparisons from the
Scholar 6 weeks ago, created an answer that has been accepted. For A: trouble installing DESeq2
Appreciated 8 weeks ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 8 weeks ago, created an answer that has been accepted. For A: trouble installing DESeq2
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: DESeq2 rlog function takes too long
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: DESeq2: add annotations (from data frame) to DESeqDataSet
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: DESeq is better than DESeq2?
Scholar 11 months ago, created an answer that has been accepted. For A: PCA from deseq and r function differ
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: deseq2 estimating size factors

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