Moderator: Michael Love

gravatar for Michael Love
Michael Love10k
Reputation:
10,150
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
Last seen:
5 hours ago
Joined:
3 years, 10 months ago
Email:
m****************@gmail.com

I'm an Assistant Professor in the Department of Biostatistics at UNC Chapel Hill.

My main Bioconductor involvement is to maintain these software packages:

 

Posts by Michael Love

<prev • 1,835 results • page 1 of 184 • next >
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Answer: A: RNA-seq workflow at the gene level - "colSums(assay(se))" command ?
... A quick note about the support site: I won't get a notification to check here unless you use a specific tag related to the workflow or a package I maintain: "If you have questions about this workflow or any Bioconductor software, please post these to the Bioconductor support site. If the questions ...
written 9 hours ago by Michael Love10k
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Comment: C: tximport RSEM error
... I changed my answer as 'l' is a vector. ...
written 22 hours ago by Michael Love10k
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Answer: A: tximport RSEM error
... What is 'l'? Can you show the top of one of the files: readLines(l[1], n=10) ...
written 22 hours ago by Michael Love10k
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Comment: C: DEseq2 for several experiments with one condition
... You should be able to make the experiment column like so: dds$experiment <- factor(substr(colnames(dds), 1, 1)) This says to R, take the first letter from the column names (the names of the samples in your dds object), and turn this into a factor, and assign it as a new column in my colData. ...
written 1 day ago by Michael Love10k
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Comment: C: DEseq2 for several experiments with one condition
... Yes, I'll say that things are being stated to vaguely for me to give a more useful response. And I don't have time to coax additional information from the OP. The approach above makes the assumption that the fixed treatment effect is the same across the experiments, and allows for an experiment-sp ...
written 2 days ago by Michael Love10k
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Comment: C: DEseq2 for several experiments with one condition
... The easiest way to get an average treatment effect would be to use a design of ~experiment + condition, and then build the results table for condition (see the DESeq2 vignette or ?results). Experiment should be a factor where the levels are the letters above (A,B,C,...I), and condition should be a ...
written 2 days ago by Michael Love10k
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Answer: A: DESeq2: Is it possible to convert read counts to expression values via TPM and r
... If you had access to the FASTQ files, the best way to estimate gene-level TPM in my opinion would be to use fast, lightweight transcript abundance quantifiers like Salmon, Sailfish or kallisto (or RSEM, which is also accurate but not as fast as these other three). These are my preferred way to gener ...
written 2 days ago by Michael Love10k
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Answer: A: DEseq2 for several experiments with one condition
... Please post your column data so I have some idea what the experiment looks like. ...
written 2 days ago by Michael Love10k
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Answer: A: PCA plot in DESeq2
... I've received this question before on the support site, and my answer is that I really don't understand the point of a PCA plot in which you can't see how the samples within a group spread out. I suppose you can compare the distances between 3 or more conditions, but those distances relative to the ...
written 4 days ago by Michael Love10k
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Answer: A: Contrast analysis for A B or B A
... This section of the workflow might be useful for you, describing fold changes and the meaning of the results table: http://www.bioconductor.org/help/workflows/rnaseqGene/#building-the-results-table ...
written 6 days ago by Michael Love10k

Latest awards to Michael Love

Appreciated 9 months ago, created a post with more than 5 votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Good Question 9 months ago, asked a question that was upvoted at least 5 times. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Student 9 months ago, asked a question with at least 3 up-votes. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling)
Scholar 9 months ago, created an answer that has been accepted. For A: DESeq2 Design with Multiple Interactions
Scholar 9 months ago, created an answer that has been accepted. For A: DESeq2 Design with Multiple Interactions
Scholar 9 months ago, created an answer that has been accepted. For A: DESeq2 Design with Multiple Interactions
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: deseq2 estimating size factors
Scholar 9 months ago, created an answer that has been accepted. For A: DESeq2 Design with Multiple Interactions
Scholar 9 months ago, created an answer that has been accepted. For A: DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: DESeq is better than DESeq2?
Voter 9 months ago, voted more than 100 times.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: DESeq is better than DESeq2?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: CPM filtering in deseq2
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: CPM filtering in deseq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: CPM filtering in deseq2
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
Popular Question 10 months ago, created a question with more than 1,000 views. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq)
Scholar 10 months ago, created an answer that has been accepted. For A: DESeq2/SAMSeq - analysing subset of genes from RNASeq dataset
Good Question 10 months ago, asked a question that was upvoted at least 5 times. For DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq)
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: DESeq2 rlog error
Scholar 11 months ago, created an answer that has been accepted. For A: Using DESeq2 after agglomerating OTUs
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: DESeq2 rlog error

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