Moderator: Michael Love

gravatar for Michael Love
Michael Love23k
Reputation:
22,980
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Trusted
Location:
United States
Website:
http://mikelove.github...
Twitter:
mikelove
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Google Scholar Page
Last seen:
an hour ago
Joined:
6 years, 2 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 • 4,733 results • page 2 of 474 • next >
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Comment: C: Three-factor design with DESeq2
... Please consult with a statistician for further explanation of the terms in an interaction model, beyond the sections of the vignette and workflow, I think if users are still not sure what is represented by the coefficients, they really should be collaborating to make sure they get it correct. ...
written 3 days ago by Michael Love23k
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Answer: A: Phylpseq to deseq2
... Again, take a look at the vignette and beginners workflow, which explain the LFC in detail. ...
written 3 days ago by Michael Love23k
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Comment: C: DESeq not showing all coefficient
... Take a look at the vignette and the workflow for beginners. The meaning of the LFC is explained in detail. ...
written 3 days ago by Michael Love23k
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Answer: A: DESeq2 complex model matrix and result interpretations
... A few notes: The re-factoring has to happen before you run `model.matrix`. Right now you are getting pre vs post, but if you fix this, it will be post vs pre. The second and third results tables are correct. The first results table can't really be formed with this design, because you want to cont ...
written 3 days ago by Michael Love23k
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Comment: C: Correct use of tximport in combination with edgeR cpm()
... hi Aaron and AT, I'll add this to the tximport vignette if Aaron gives the ok. I'm just less knowledgeable about internals so want to make sure I don't promulgate something not accurate. ...
written 4 days ago by Michael Love23k
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Comment: C: Complex Design matrix for DE analysis
... Rather than continuing to send alerts to the limma and edgeR maintainers, for additional questions specific to DESeq2 could you make a new post? ...
written 4 days ago by Michael Love23k
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Comment: C: Plot genes with similar expression patterns
... Go for it. I have made these plots manually one time using base R: `hclust, dist, rowMeans, lines`, etc., but we don't have example code for this in the vignette. ...
written 4 days ago by Michael Love23k
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Answer: A: Plot genes with similar expression patterns
... I would start by computing the VST: ``` vsd <- vst(dds) ``` And then you can perform hierarchical clustering after computing Euclidean distance between genes. You can remove the row mean from each row, so that the baseline expression doesn't factor in. ...
written 4 days ago by Michael Love23k
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Comment: C: Correct use of tximport in combination with edgeR cpm()
... This is beyond my knowledge of edgeR. I checked that chunk of tximport vignette code with Aaron at some point, to make sure we were doing it properly. ...
written 4 days ago by Michael Love23k
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Answer: A: Tximport and pseudo alignment with Kallisto
... Your first line of code above is mistakenly collapsing multiple biological replicates into a single sample. As you say in your question the option to give multiple input files is for usage with technical replicates only. ...
written 4 days ago by Michael Love23k

Latest awards to Michael Love

Scholar 4 months ago, created an answer that has been accepted. For A: DESeq2 why estimate dispersion on log scale
Scholar 4 months ago, created an answer that has been accepted. For A: Unexpected differences in results from paired analysis with DESeq2
Scholar 4 months ago, created an answer that has been accepted. For A: Add new columns to DESeqResults from text file by matching rownames.
Scholar 4 months ago, created an answer that has been accepted. For A: DESeq2 comparing differential expression results
Scholar 4 months ago, created an answer that has been accepted. For A: DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
Scholar 4 months ago, created an answer that has been accepted. For A: Age covariate continuous vs. categorical
Scholar 4 months ago, created an answer that has been accepted. For A: Altering design following DESeqDataSetFromMatrix and DESeq
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: How does DESeq2 handle zero counts in one condition?
Scholar 4 months ago, created an answer that has been accepted. For A: calculate foldchange after rlogTransformation
Scholar 4 months ago, created an answer that has been accepted. For A: tximport error: all(names(aveLengthSampGene) == rownames(lengthMat)) is not TRUE
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: DESeq2 baseMean values for each sample
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: [DESeq2] time series strain-specific differences over time
Scholar 4 months ago, created an answer that has been accepted. For A: DESEQ2 design with multiple conditions
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: clarification of time-series analysis
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
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Normalization using DESeq
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: [DESEQ2] How to access the normalized data of a DESeqDataSet
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: DEseq2 - Use normalized DEseq2 counts to plot most expressed genes per group
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: DESeq2 why estimate dispersion on log scale
Scholar 4 months ago, created an answer that has been accepted. For A: Get the countsFromAbundance as limma input
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What doest this p.value distribution mean?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Common differentially expressed genes between two cell lines
Scholar 4 months ago, created an answer that has been accepted. For A: Common differentially expressed genes between two cell lines
Scholar 4 months ago, created an answer that has been accepted. For A: Get release date for version of DESeq2

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